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Extracellular Vesicles in Phylogeny

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

Deadline for manuscript submissions: closed (31 August 2021) | Viewed by 33741

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Guest Editor
Pathobiology and Extracellular Vesicle Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK
Interests: peptidylarginine deiminases; tissue remodelling; extracellular vesicles; CNS regeneration; cancer; mucosal immunity; innate immunity; stem cells
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Special Issue Information

Dear Colleagues,

Extracellular vesicles are 20–1000 nm lipid vesicles (also commonly called exosomes and microvesicles) which are released from most cells and participate in cellular communication in health and disease via transport of a genetic and protein cargo. EVs can be isolated from a range of body fluids and are therefore also valuable health- and pathology-related biomarkers.  A large body of work has been carried out on the functions of EVs in a range of pathological processes and in normal physiology, while relatively less is known about the diversity of EVs and EV-mediated roles across phylogeny.

This Special Issue aims to collect state-of-the-art primary research studies and review articles from international experts and diverse leading groups in the EV field to update our current understanding of EVs in diverse taxa from bacteria to mammals, including humans. The focus will be on elucidating the multifaceted roles of EVs, including their potential for biomarker discovery, veterinary research, wildlife research and conservation, and research in bacterial communication, zoonotic disease, infectious disease, and host–pathogen interactions. Research on EVs using comparative animal models to study human pathologies as well as unusual metabolic and immunological traits that can inform longevity, disease resistance, and health, are also welcome.

Dr. Sigrun Lange
Guest Editor

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Keywords

  • Extracellular vesicles
  • Phylogeny
  • Immunology
  • Infectious disease
  • Metabolism
  • Longevity
  • Disease resistance
  • Cancer resistance
  • Antibiotic resistance
  • Zoonotic disease
  • Host-pathogen interactions
  • Pathology
  • Veterinary research
  • Wildlife conservation
  • Comparative animal models
  • Biomarkers

Published Papers (8 papers)

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Research

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14 pages, 3555 KiB  
Article
Fatty Acid Unsaturation Degree of Plasma Exosomes in Colorectal Cancer Patients: A Promising Biomarker
by Joan Bestard-Escalas, Rebeca Reigada, José Reyes, Paloma de la Torre, Gerhard Liebisch and Gwendolyn Barceló-Coblijn
Int. J. Mol. Sci. 2021, 22(10), 5060; https://doi.org/10.3390/ijms22105060 - 11 May 2021
Cited by 19 | Viewed by 2557
Abstract
Even though colorectal cancer (CRC) is one of the most preventable cancers, it is currently one of the deadliest. Worryingly, incidence in people <50 years has increased unexpectedly, and for unknown causes, despite the successful implementation of screening programs in the population aged [...] Read more.
Even though colorectal cancer (CRC) is one of the most preventable cancers, it is currently one of the deadliest. Worryingly, incidence in people <50 years has increased unexpectedly, and for unknown causes, despite the successful implementation of screening programs in the population aged >50 years. Thus, there is a need to improve early diagnosis detection strategies by identifying more precise biomarkers. In this scenario, the analysis of exosomes is given considerable attention. Previously, we demonstrated the exosome lipidome was able to classify CRC cell lines according to their malignancy. Herein, we investigated the use of the lipidome of plasma extracellular vesicles as a potential source of non-invasive biomarkers for CRC. A plasma exosome-enriched fraction was analyzed from patients undergoing colonoscopic procedure. Patients were divided into a healthy group and four pathological groups (patients with hyperplastic polyps; adenomatous polyps; invasive neoplasia (CRC patients); or hereditary non-polyposis CRC. The results showed a shift from 34:1- to 38:4-containing species in the pathological groups. We demonstrate that the ratio Σ34:1-containing species/Σ38:4-containing species has the potential to discriminate between healthy and pathological patients. Altogether, the results reinforce the utility of plasma exosome lipid fingerprint to provide new non-invasive biomarkers in a clinical context. Full article
(This article belongs to the Special Issue Extracellular Vesicles in Phylogeny)
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36 pages, 6128 KiB  
Article
The Proteome and Citrullinome of Hippoglossus hippoglossus Extracellular Vesicles—Novel Insights into Roles of the Serum Secretome in Immune, Gene Regulatory and Metabolic Pathways
by Bergljót Magnadóttir, Igor Kraev, Alister W. Dodds and Sigrun Lange
Int. J. Mol. Sci. 2021, 22(2), 875; https://doi.org/10.3390/ijms22020875 - 16 Jan 2021
Cited by 8 | Viewed by 2943
Abstract
Extracellular vesicles (EVs) are lipid bilayer vesicles which are released from cells and play multifaceted roles in cellular communication in health and disease. EVs can be isolated from various body fluids, including serum and plasma, and are usable biomarkers as they can inform [...] Read more.
Extracellular vesicles (EVs) are lipid bilayer vesicles which are released from cells and play multifaceted roles in cellular communication in health and disease. EVs can be isolated from various body fluids, including serum and plasma, and are usable biomarkers as they can inform health status. Studies on EVs are an emerging research field in teleost fish, with accumulating evidence for important functions in immunity and homeostasis, but remain to be characterised in most fish species, including halibut. Protein deimination is a post-translational modification caused by a conserved family of enzymes, named peptidylarginine deiminases (PADs), and results in changes in protein folding and function via conversion of arginine to citrulline in target proteins. Protein deimination has been recently described in halibut ontogeny and halibut serum. Neither EV profiles, nor total protein or deiminated protein EV cargos have yet been assessed in halibut and are reported in the current study. Halibut serum EVs showed a poly-dispersed population in the size range of 50–600 nm, with modal size of EVs falling at 138 nm, and morphology was further confirmed by transmission electron microscopy. The assessment of EV total protein cargo revealed 124 protein hits and 37 deiminated protein hits, whereof 15 hits were particularly identified in deiminated form only. Protein interaction network analysis showed that deimination hits are involved in a range of gene regulatory, immune, metabolic and developmental processes. The same was found for total EV protein cargo, although a far wider range of pathways was found than for deimination hits only. The expression of complement component C3 and C4, as well as pentraxin-like protein, which were identified by proteomic analysis, was further verified in EVs by western blotting. This showed that C3 is exported in EVs at higher levels than C4 and deiminated C3 was furthermore confirmed to be at high levels in the deimination-enriched EV fractions, while, in comparison, C4 showed very low detection in deimination-enriched EV fractions. Pentraxin was exported in EVs, but not detected in the deimination-enriched fractions. Our findings provide novel insights into EV-mediated communication in halibut serum, via transport of protein cargo, including post-translationally deiminated proteins. Full article
(This article belongs to the Special Issue Extracellular Vesicles in Phylogeny)
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19 pages, 2394 KiB  
Article
Comparative Lipidomic Analysis of Extracellular Vesicles Derived from Lactobacillus plantarum APsulloc 331261 Living in Green Tea Leaves Using Liquid Chromatography-Mass Spectrometry
by Hyoseon Kim, Minjung Kim, Kilsun Myoung, Wanil Kim, Jaeyoung Ko, Kwang Pyo Kim and Eun-Gyung Cho
Int. J. Mol. Sci. 2020, 21(21), 8076; https://doi.org/10.3390/ijms21218076 - 29 Oct 2020
Cited by 16 | Viewed by 3768
Abstract
Lactobacillus plantarum is a popular probiotic species due to its safe and beneficial effects on humans; therefore, novel L. plantarum strains have been isolated and identified from various dietary products. Given that bacteria-derived extracellular vesicles (EVs) have been considered as efficient carriers of [...] Read more.
Lactobacillus plantarum is a popular probiotic species due to its safe and beneficial effects on humans; therefore, novel L. plantarum strains have been isolated and identified from various dietary products. Given that bacteria-derived extracellular vesicles (EVs) have been considered as efficient carriers of bioactive materials and shown to evoke cellular responses effectively, L. plantarum-derived EVs are expected to efficiently elicit health benefits. Herein, we identified L. plantarum APsulloc 331261 living in green tea leaves and isolated EVs from the culture medium. We performed quantitative lipidomic analysis of L. plantarum APsulloc 331261 derived EVs (LEVs) using liquid chromatography-mass spectrometry. In comparison to L. plantarum APsulloc 331261, in LEVs, 67 of 320 identified lipid species were significantly increased and 19 species were decreased. In particular, lysophosphatidylserine(18:4) and phosphatidylcholine(32:2) were critically increased, showing over 21-fold enrichment in LEVs. In addition, there was a notable difference between LEVs and the parent cells in the composition of phospholipids. Our results suggest that the lipidomic profile of bacteria-derived EVs is different from that of the parent cells in phospholipid content and composition. Given that lipids are important components of EVs, quantitative and comparative analyses of EV lipids may improve our understanding of vesicle biogenesis and lipid-mediated intercellular communication within or between living organisms. Full article
(This article belongs to the Special Issue Extracellular Vesicles in Phylogeny)
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42 pages, 6970 KiB  
Article
Post-Translational Protein Deimination Signatures in Serum and Serum-Extracellular Vesicles of Bos taurus Reveal Immune, Anti-Pathogenic, Anti-Viral, Metabolic and Cancer-Related Pathways for Deimination
by Michael F. Criscitiello, Igor Kraev and Sigrun Lange
Int. J. Mol. Sci. 2020, 21(8), 2861; https://doi.org/10.3390/ijms21082861 - 19 Apr 2020
Cited by 17 | Viewed by 5393
Abstract
The bovine immune system is known for its unusual traits relating to immunoglobulin and antiviral responses. Peptidylarginine deiminases (PADs) are phylogenetically conserved enzymes that cause post-translational deimination, contributing to protein moonlighting in health and disease. PADs also regulate extracellular vesicle (EV) release, forming [...] Read more.
The bovine immune system is known for its unusual traits relating to immunoglobulin and antiviral responses. Peptidylarginine deiminases (PADs) are phylogenetically conserved enzymes that cause post-translational deimination, contributing to protein moonlighting in health and disease. PADs also regulate extracellular vesicle (EV) release, forming a critical part of cellular communication. As PAD-mediated mechanisms in bovine immunology and physiology remain to be investigated, this study profiled deimination signatures in serum and serum-EVs in Bos taurus. Bos EVs were poly-dispersed in a 70–500 nm size range and showed differences in deiminated protein cargo, compared with whole sera. Key immune, metabolic and gene regulatory proteins were identified to be post-translationally deiminated with some overlapping hits in sera and EVs (e.g., immunoglobulins), while some were unique to either serum or serum-EVs (e.g., histones). Protein–protein interaction network analysis of deiminated proteins revealed KEGG pathways common for serum and serum-EVs, including complement and coagulation cascades, viral infection (enveloped viruses), viral myocarditis, bacterial and parasitic infections, autoimmune disease, immunodeficiency intestinal IgA production, B-cell receptor signalling, natural killer cell mediated cytotoxicity, platelet activation and hematopoiesis, alongside metabolic pathways including ferroptosis, vitamin digestion and absorption, cholesterol metabolism and mineral absorption. KEGG pathways specific to EVs related to HIF-1 signalling, oestrogen signalling and biosynthesis of amino acids. KEGG pathways specific for serum only, related to Epstein–Barr virus infection, transcription mis-regulation in cancer, bladder cancer, Rap1 signalling pathway, calcium signalling pathway and ECM-receptor interaction. This indicates differences in physiological and pathological pathways for deiminated proteins in serum-EVs, compared with serum. Our findings may shed light on pathways underlying a number of pathological and anti-pathogenic (viral, bacterial, parasitic) pathways, with putative translatable value to human pathologies, zoonotic diseases and development of therapies for infections, including anti-viral therapies. Full article
(This article belongs to the Special Issue Extracellular Vesicles in Phylogeny)
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37 pages, 7454 KiB  
Article
Protein Deimination Signatures in Plasma and Plasma-EVs and Protein Deimination in the Brain Vasculature in a Rat Model of Pre-Motor Parkinson’s Disease
by Marco Sancandi, Pinar Uysal-Onganer, Igor Kraev, Audrey Mercer and Sigrun Lange
Int. J. Mol. Sci. 2020, 21(8), 2743; https://doi.org/10.3390/ijms21082743 - 15 Apr 2020
Cited by 23 | Viewed by 5611
Abstract
The identification of biomarkers for early diagnosis of Parkinson’s disease (PD) is of pivotal importance for improving approaches for clinical intervention. The use of translatable animal models of pre-motor PD therefore offers optimal opportunities for novel biomarker discovery in vivo. Peptidylarginine deiminases (PADs) [...] Read more.
The identification of biomarkers for early diagnosis of Parkinson’s disease (PD) is of pivotal importance for improving approaches for clinical intervention. The use of translatable animal models of pre-motor PD therefore offers optimal opportunities for novel biomarker discovery in vivo. Peptidylarginine deiminases (PADs) are a family of calcium-activated enzymes that contribute to protein misfolding through post-translational deimination of arginine to citrulline. Furthermore, PADs are an active regulator of extracellular vesicle (EV) release. Both protein deimination and extracellular vesicles (EVs) are gaining increased attention in relation to neurodegenerative diseases, including in PD, while roles in pre-motor PD have yet to be investigated. The current study aimed at identifying protein candidates of deimination in plasma and plasma-EVs in a rat model of pre-motor PD, to assess putative contributions of such post-translational changes in the early stages of disease. EV-cargo was further assessed for deiminated proteins as well as three key micro-RNAs known to contribute to inflammation and hypoxia (miR21, miR155, and miR210) and also associated with PD. Overall, there was a significant increase in circulating plasma EVs in the PD model compared with sham animals and inflammatory and hypoxia related microRNAs were significantly increased in plasma-EVs of the pre-motor PD model. A significantly higher number of protein candidates were deiminated in the pre-motor PD model plasma and plasma-EVs, compared with those in the sham animals. KEGG (Kyoto encyclopedia of genes and genomes) pathways identified for deiminated proteins in the pre-motor PD model were linked to “Alzheimer’s disease”, “PD”, “Huntington’s disease”, “prion diseases”, as well as for “oxidative phosphorylation”, “thermogenesis”, “metabolic pathways”, “Staphylococcus aureus infection”, gap junction, “platelet activation”, “apelin signalling”, “retrograde endocannabinoid signalling”, “systemic lupus erythematosus”, and “non-alcoholic fatty liver disease”. Furthermore, PD brains showed significantly increased staining for total deiminated proteins in the brain vasculature in cortex and hippocampus, as well as increased immunodetection of deiminated histone H3 in dentate gyrus and cortex. Our findings identify EVs and post-translational protein deimination as novel biomarkers in early pre-motor stages of PD. Full article
(This article belongs to the Special Issue Extracellular Vesicles in Phylogeny)
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Review

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28 pages, 1767 KiB  
Review
Extracellular Vesicles in the Fungi Kingdom
by Marc Liebana-Jordan, Bruno Brotons, Juan Manuel Falcon-Perez and Esperanza Gonzalez
Int. J. Mol. Sci. 2021, 22(13), 7221; https://doi.org/10.3390/ijms22137221 - 5 Jul 2021
Cited by 34 | Viewed by 5236
Abstract
Extracellular vesicles (EVs) are membranous, rounded vesicles released by prokaryotic and eukaryotic cells in their normal and pathophysiological states. These vesicles form a network of intercellular communication as they can transfer cell- and function-specific information (lipids, proteins and nucleic acids) to different cells [...] Read more.
Extracellular vesicles (EVs) are membranous, rounded vesicles released by prokaryotic and eukaryotic cells in their normal and pathophysiological states. These vesicles form a network of intercellular communication as they can transfer cell- and function-specific information (lipids, proteins and nucleic acids) to different cells and thus alter their function. Fungi are not an exception; they also release EVs to the extracellular space. The vesicles can also be retained in the periplasm as periplasmic vesicles (PVs) and the cell wall. Such fungal vesicles play various specific roles in the lives of these organisms. They are involved in creating wall architecture and maintaining its integrity, supporting cell isolation and defence against the environment. In the case of pathogenic strains, they might take part in the interactions with the host and affect the infection outcomes. The economic importance of fungi in manufacturing high-quality nutritional and pharmaceutical products and in remediation is considerable. The analysis of fungal EVs opens new horizons for diagnosing fungal infections and developing vaccines against mycoses and novel applications of nanotherapy and sensors in industrial processes. Full article
(This article belongs to the Special Issue Extracellular Vesicles in Phylogeny)
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15 pages, 880 KiB  
Review
Exosomal Cargo May Hold the Key to Improving Reproductive Outcomes in Dairy Cows
by Natalie Turner, Pevindu Abeysinghe, Pawel Sadowski and Murray D. Mitchell
Int. J. Mol. Sci. 2021, 22(4), 2024; https://doi.org/10.3390/ijms22042024 - 18 Feb 2021
Cited by 6 | Viewed by 2861
Abstract
The reproductive status of dairy cows remains a challenge for dairy farmers worldwide, with impaired fertility linked to a significant reduction in herd profitability, due in part to impaired immunity, increased metabolic pressure, and longer postpartum anestrous interval (PPAI). Exosomes are nanovesicles released [...] Read more.
The reproductive status of dairy cows remains a challenge for dairy farmers worldwide, with impaired fertility linked to a significant reduction in herd profitability, due in part to impaired immunity, increased metabolic pressure, and longer postpartum anestrous interval (PPAI). Exosomes are nanovesicles released from a variety of cell types and end up in circulation, and carry proteins, bioactive peptides, lipids, and nucleic acids specific to the place of origin. As such, their role in health and disease has been investigated in humans and animals. This review discusses research into exosomes in the context of reproduction in dairy herds and introduces recent advances in mass-spectrometry (MS) based proteomics that have a potential to advance quantitative profiling of exosomal protein cargo in a search for early biomarkers of cattle fertility. Full article
(This article belongs to the Special Issue Extracellular Vesicles in Phylogeny)
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16 pages, 1255 KiB  
Review
The Role of Exosomal Epigenetic Modifiers in Cell Communication and Fertility of Dairy Cows
by Pevindu Abeysinghe, Natalie Turner, Isabella Morean Garcia, Eman Mosaad, Hassendrini N. Peiris and Murray D. Mitchell
Int. J. Mol. Sci. 2020, 21(23), 9106; https://doi.org/10.3390/ijms21239106 - 30 Nov 2020
Cited by 10 | Viewed by 4410
Abstract
Abnormal uterine function affects conception rate and embryo development, thereby leading to poor fertility and reproduction failure. Exosomes are a nanosized subclass of extracellular vesicles (EV) that have important functions as intercellular communicators. They contain and carry transferable bioactive substances including micro RNA [...] Read more.
Abnormal uterine function affects conception rate and embryo development, thereby leading to poor fertility and reproduction failure. Exosomes are a nanosized subclass of extracellular vesicles (EV) that have important functions as intercellular communicators. They contain and carry transferable bioactive substances including micro RNA (miRNA) for target cells. Elements of the cargo can provide epigenetic modifications of the recipient cells and may have crucial roles in mechanisms of reproduction. The dairy industry accounts for a substantial portion of the economy of many agricultural countries. Exosomes can enhance the expression of inflammatory mediators in the endometrium, which contribute to various inflammatory diseases in transition dairy cows. This results in reduced fertility which leads to reduced milk production and increased cow maintenance costs. Thus, gaining a clear knowledge of exosomal epigenetic modifiers is critical to improving the breeding success and profitability of dairy farms. This review provides a brief overview of how exosomal miRNA contributes to inflammatory diseases and hence to poor fertility, particularly in dairy cows. Full article
(This article belongs to the Special Issue Extracellular Vesicles in Phylogeny)
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