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New Challenges and Opportunities: Extracellular Vesicles in Biological and Biochemical Processes, 2nd Edition

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

Deadline for manuscript submissions: 20 June 2026 | Viewed by 11323

Special Issue Editors

Dr. Ilaria Giusti

E-Mail Website
Guest Editor
Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
Interests: extracellular vesicles; tumor microenvironment; angiogenesis; platelet derivatives; regenerative medicine
Special Issues, Collections and Topics in MDPI journals
Dr. Celeste Caruso Bavisotto

E-Mail Website
Guest Editor
Department of Biomedicine, Neurosciences and Advanced Diagnostic (BiND), Human Anatomy Section, University of Palermo, 90127 Palermo, Italy
Interests: cell differentiation; tissue homeostasis; organ remodeling; organ-on-chip; cell stress; chaperones; heat shock proteins; chaperonopathies; exosomes; glioblastoma
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Cell-to-cell communication is mediated by the release of a plethora of soluble molecules of varying nature and functions. However, extracellular vesicles (EVs) have been recognized as essential mediators of this intercellular crosstalk for many years now, being involved in all key biological processes in humans, such as cell differentiation, tissue homeostasis, and organ remodeling.

EVs are membrane-enclosed structures, containing a complex cargo composed of proteins, lipids, and nucleic acids, which can be fully functional once transferred to target cells, and when released by normal and tumor cells, they act as critical modulators in both physiological and pathological conditions.

This Special Issue, “New Challenges and Opportunities: Extracellular Vesicles in Biological and Biochemical Processes”, will comprise a selection of research papers and reviews, focusing on the novel biochemical and molecular aspects of biological processes mediated by EVs. Contributions are welcome on EVs molecular characterization and cell signaling pathways involved in EVs-mediated physiological and pathological processes, as well as their impact on possible clinical implications.

Dr. Ilaria Giusti
Dr. Celeste Caruso Bavisotto
Guest Editors

Manuscript Submission Information

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • extracellular vesicles
  • exosomes intercellular
  • crosstalk liquid biopsy carcinogenesis
  • cell differentiation tissue
  • homeostasis
  • organ remodeling
  • biomedicine
  • advanced diagnostics

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Published Papers (4 papers)

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Research

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19 pages, 6582 KB  
Article
Extracellular Vesicle and Plasma miRNAs as Candidate Biomarkers of Traumatic Brain Injury in the Context of Polytrauma
by Cora Rebecca Schindler, Dirk Henrich, Lena Krämer, Inna Schaible, Jason-Alexander Hörauf, Aileen Ritter, Philipp Störmann, Rald Victor Maria Groven, Markus Huber-Lang, Ingo Marzi and Liudmila Leppik
Int. J. Mol. Sci. 2026, 27(10), 4248; https://doi.org/10.3390/ijms27104248 - 10 May 2026
Viewed by 362
Abstract
Severe traumatic brain injury (TBI) is a leading cause of mortality and long-term disability in polytrauma (PT) patients, and its clinical outcome remains difficult to predict due to clinical heterogeneity and secondary injury mechanisms. Current diagnostic and prognostic approaches based on clinical assessment [...] Read more.
Severe traumatic brain injury (TBI) is a leading cause of mortality and long-term disability in polytrauma (PT) patients, and its clinical outcome remains difficult to predict due to clinical heterogeneity and secondary injury mechanisms. Current diagnostic and prognostic approaches based on clinical assessment and imaging are limited, particularly in PT where neurological evaluation is often impaired. This study aimed to compare plasma- and extracellular vesicle (EV)-associated microRNA (miRNA) signatures in patients with severe TBI and healthy controls to identify their potential as minimally invasive biomarkers and to improve understanding of molecular responses. For profiling circulating miRNAs, blood samples were collected at ≤3 h and at 48 h after admission. In the screening phase, plasma samples of n = 15 patients with severe isolated TBI (Abbreviated Injury Scale [AIS]Head ≥ 4, all other AIS ≤ 1) and n = 15 age- and sex-matched healthy controls were pooled (n = 5/pool) and subjected to next-generation sequencing (NGS). In the following validation phase, n = 25 severely injured trauma patients (Injury Severity Score [ISS] ≥ 16) were enrolled and stratified into PT without TBI (PT; AISHead = 0; n = 13) and isolated TBI (n = 12). Differentially expressed candidate miRNAs identified in the screening phase were validated in individual plasma and EV samples using reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Functional enrichment and pathway analyses were performed using miRNet. NGS identified more differentially expressed miRNAs in plasma (ER: 103; 48 h: 65) than in EVs (Emergency Room [ER]: 14; 48 h: 32). Functional enrichment analysis indicated associations with pathways related to cellular stress, senescence, growth factor signaling, transcriptional regulation, and apoptosis. In validation, 12 of 16 plasma and 10 of 15 EV-miRNAs were confirmed as differentially expressed in TBI patients; among these, three plasma and four EV miRNAs differed between TBI and PT. After adjustment, most plasma miRNAs were associated with injury severity rather than group status. EV miRNA profiles showed heterogeneous patterns, with miR-1469 associated with TBI group status in adjusted analysis, while miR-1237-5p was linked to injury severity and other EV miRNAs showed no consistent group-specific effects. Plasma miRNAs mainly correlated with systemic injury markers, whereas EV miR-1469 showed a moderate association with the Glasgow Coma Scale (GCS). Overall, circulating miRNA profiles after injury appear to be predominantly influenced by systemic trauma severity rather than TBI-specific effects. Plasma miRNAs mainly reflected general injury burden, whereas EV-associated miRNAs showed more heterogeneous patterns, with miR-1469 emerging as a candidate associated with TBI after adjustment for clinical covariates. These findings suggest that EV-derived miRNAs, particularly miR-1469, may provide more targeted signals related to brain injury and warrant further investigation. Full article
(This article belongs to the Special Issue New Challenges and Opportunities: Extracellular Vesicles in Biological and Biochemical Processes, 2nd Edition)
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14 pages, 1489 KB  
Article
Protocols for Extraction of miRNA from Extracellular Vesicles of Lyophilized Human Saliva Samples
by Valquiria Quinelato, Carlos Fernando Mourão, Thalita Alves Barreto Santos, Patrícia Cataldo de Felipe Cordeiro, Leticia Ladeira Bonato, Miria Gomes Pereira, Jose Albuquerque Calasans-Maia, Jose Mauro Granjeiro, Tomoyuki Kawase and Priscila Ladeira Casado
Int. J. Mol. Sci. 2025, 26(7), 2891; https://doi.org/10.3390/ijms26072891 - 22 Mar 2025
Cited by 1 | Viewed by 2710
Abstract
Extracellular vesicles (EVs) are emerging as crucial biomarkers in molecular diagnostics, providing early detection of disease progression. Although ultracentrifugation remains the gold standard for vesicle isolation from biofluids, it has limitations in scalability and accessibility. This study presents lyophilization as an innovative method [...] Read more.
Extracellular vesicles (EVs) are emerging as crucial biomarkers in molecular diagnostics, providing early detection of disease progression. Although ultracentrifugation remains the gold standard for vesicle isolation from biofluids, it has limitations in scalability and accessibility. This study presents lyophilization as an innovative method for preserving EVs and isolating microRNAs from saliva, utilizing its proven ability to maintain biological activity and prevent unwanted chemical reactions. We assessed five different sample preparation protocols combined with a dual-purification strategy. Structural and molecular integrity analyses revealed that lyophilized samples retained essential EV characteristics, including CD63/CD9 membrane localization. QELS analysis and electron microscopy confirmed distinct vesicle populations in both ultracentrifuged (30–50 nm and 320–360 nm) and lyophilized samples (50–70 nm and 360–380 nm). Importantly, lyophilized samples exhibited higher total RNA concentrations (p < 0.0001) while preserving key microRNA signatures (miR-16, miR-21, miR-33a, and miR-146b) with high fidelity. The efficacy of lyophilization is linked to its ability to systematically reduce solvent content through sublimation while maintaining vesicle integrity and molecular cargo. This method offers a practical, scalable alternative for EV isolation with significant implications for biomarker-based diagnostics. Full article
(This article belongs to the Special Issue New Challenges and Opportunities: Extracellular Vesicles in Biological and Biochemical Processes, 2nd Edition)
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13 pages, 596 KB  
Brief Report
Expression of Serum and Exosomal microRNA-34a in Subjects with Increased Fat Mass
by Jacqueline Alejandra Noboa-Velástegui, Rodolfo Iván Valdez-Vega, Jorge Castro-Albarran, Perla Monserrat Madrigal-Ruiz, Ana Lilia Fletes-Rayas, Sandra Luz Ruiz-Quezada, Martha Eloisa Ramos-Márquez, José de Jesús López-Jiménez, Iñaki Álvarez and Rosa Elena Navarro-Hernández
Int. J. Mol. Sci. 2026, 27(1), 270; https://doi.org/10.3390/ijms27010270 - 26 Dec 2025
Cited by 1 | Viewed by 946
Abstract
Extracellular vesicles (EVs), particularly exosomes, are key mediators of intercellular communication, transporting biomolecules such as nucleic acids, lipids, and proteins that influence immune and metabolic pathways. In adipose tissue (AT), adipocyte-derived EVs (AdEVs) play a crucial role in maintaining metabolic homeostasis and have [...] Read more.
Extracellular vesicles (EVs), particularly exosomes, are key mediators of intercellular communication, transporting biomolecules such as nucleic acids, lipids, and proteins that influence immune and metabolic pathways. In adipose tissue (AT), adipocyte-derived EVs (AdEVs) play a crucial role in maintaining metabolic homeostasis and have been implicated in obesity-related dysfunction. Among their bioactive cargo, microRNAs regulate post-transcriptional gene expression and participate in immunometabolic regulation. This study aimed to determine whether miR-34a expression in serum and circulating EVs varies according to body fat percentage, to explore its potential utility as a non-invasive biomarker of AT dysfunction. A total of 142 adults (mean age 36 ± 11 years) were classified by body fat percentage (≥25% in men, ≥35% in women). Exosomes were isolated (Invitrogen®) and characterized by cryo-TEM, and miR-34a expression was quantified by qRT-PCR. miR-34a expression correlated negatively with Total Cholesterol, Triglycerides, LDLc/HDLc, TG/HDLc, BMI, C3, CRP, fasting insulin, HOMA-IR, HOMA-B, Body adiposity, Chemerin, CCL2, AdipoQT, and AdipoQ-H, but positively with HDLc and QUICKI. Notably, LDLc, sdLDLc, sdLDLc/LDLc, TC/HDLc, and fasting glucose showed opposite correlation patterns between serum and exosomes. Overall, serum miR-34a levels were higher than in exosomes, suggesting its potential as a biomarker of metabolic dysfunction and insulin resistance. Full article
(This article belongs to the Special Issue New Challenges and Opportunities: Extracellular Vesicles in Biological and Biochemical Processes, 2nd Edition)
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10 pages, 1612 KB  
Brief Report
A Simplified Method for the Isolation of Extracellular Vesicles from Probiotic Bacteria and Their Characterization
by Harshal Sawant, Ji Bihl and Alip Borthakur
Int. J. Mol. Sci. 2025, 26(3), 1058; https://doi.org/10.3390/ijms26031058 - 26 Jan 2025
Cited by 12 | Viewed by 6409
Abstract
Probiotic bacteria are normal inhabitants of a healthy human gut, conferring multiple beneficial effects on the gut and beyond. Under various disease states, the abundance and diversity of beneficial bacteria are significantly decreased, a process called dysbiosis. Among the intra- and extracellular components [...] Read more.
Probiotic bacteria are normal inhabitants of a healthy human gut, conferring multiple beneficial effects on the gut and beyond. Under various disease states, the abundance and diversity of beneficial bacteria are significantly decreased, a process called dysbiosis. Among the intra- and extracellular components of probiotics, the extracellular vesicles (EVs) secreted by them have recently garnered significant attention as potential mediators of probiotics’ effects on host health. Further, these nanosized particles that encapsulate a wide range of bioactive molecules (proteins, lipids, RNA, and DNA) are standing out as key factors that could mediate gut microbiota–host communication and confer ameliorating effects in experimental inflammatory, metabolic, and cardiovascular disease models. However, a standard protocol of EV isolation from probiotic bacteria, not varying from lab to lab, must be established to achieve consistency in the experimental results in these pre-clinical models. Our current study compared two commonly used methods for EV isolation from biological samples, ultracentrifugation and precipitation, to develop a standard protocol for isolating EVs from the probiotics Lactobacillus acidophilus (LA), a Gram-positive bacterium, and Escherichia coli Nissle (EcN), a Gram-negative bacterium. The ultracentrifugation method gave ~1.5-fold higher EV yield for both LA and EcN compared to the precipitation method. Further, EcN released a higher level of EVs compared to LA. EVs were quantified and characterized by nanoparticle-tracking analysis (NTA) and by measuring the specific surface biomarkers using Western blot. Here, we describe our standardized step-by-step protocol for isolating EVs from probiotic bacteria and their characterization. Full article
(This article belongs to the Special Issue New Challenges and Opportunities: Extracellular Vesicles in Biological and Biochemical Processes, 2nd Edition)
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