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Exosomes—3rd Edition

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: closed (20 October 2025) | Viewed by 18598

Special Issue Editor

Prof. Dr. Abdelnaby Khalyfa

E-Mail Website
Guest Editor
Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25701, USA
Interests: genetic markers; sleep apnea; exosomes; single cell; snRNA-seq; metabolic dysfunction; animal models for sleep apnea
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Intercellular Communication between neighbored and distant cells are crucial for cell survival and responding to endocrine signaling. Exosomes, a class of extracellular vesicle (EVs) involved in cell to cell communication, are released by most of all biological fluids and emerging as novel cell-cell communication mediators in physiological and pathological conditions. These exosomes differ from other EVs based on their biogenesis, release pathways, size content, and function. Furthermore, these exosomes have shown to carry cell-specific cargos such as lipids, proteins, and miRNAs, mRNAs, and other genetic materials, and can be selectively taken up by neighboring or distant cells far from their release, which may ultimately reprogram the recipient cells distal from their release. Thus, exosomes and their biologically active cargos may offer potential biomarkers of diagnosis and therapeutic targets in a range of diseases, such as chronic inflammation, obesity, cardiovascular, neurodegenerative diseases, metabolic diseases, and tumors. This special issue aims to present new knowledge and covers all the topics relevant to exosomes in human cancers, cardiovascular, obesity, sleep, and neurogenerative deficit. We invite researchers to contribute either with original research or review articles focusing on every aspect regarding the role and function of exosomes in healthy and pathological conditions including the onset and progression of cancer, sleep, and heart diseases.

Due to the success of the 1st and 2nd editions, we would like to add more results and new insights from recent research projects.

https://www.mdpi.com/journal/ijms/special_issues/exosome

https://www.mdpi.com/journal/ijms/special_issues/VD106X1HQK

You can read more my publications at the following link: https://pubmed.ncbi.nlm.nih.gov/?term=khalyfa+a%2C+exosomes&sort=date&show_snippets=off

Dr. Abdelnaby Khalyfa
Guest Editor

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 250 words) can be sent to the Editorial Office for assessment.

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 (EVs)
  • exosomes
  • cancer
  • sleep cardiovascular diseases
  • lung disease and upper airways
  • obesity
  • sleep and end-organ morbidity

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Published Papers (8 papers)

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Research

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22 pages, 3393 KB  
Article
Comprehensive Characterization and In Vitro Functionality Study of Small Extracellular Vesicles Isolated by Different Purification Methods from Mesenchymal Stem Cell Cultures
by Marta Venturella, Ali Navaei and Davide Zocco
Int. J. Mol. Sci. 2025, 26(21), 10602; https://doi.org/10.3390/ijms262110602 - 30 Oct 2025
Viewed by 1041
Abstract
Mesenchymal stem cells (MSCs) exhibit therapeutic properties, which have been attributed to their secretome, the set of secreted factors comprising cytokines, growth factors, and extracellular vesicles (EVs). In particular, small extracellular vesicles (sEVs) or exosomes, ranging between 30 nm and 120 nm in [...] Read more.
Mesenchymal stem cells (MSCs) exhibit therapeutic properties, which have been attributed to their secretome, the set of secreted factors comprising cytokines, growth factors, and extracellular vesicles (EVs). In particular, small extracellular vesicles (sEVs) or exosomes, ranging between 30 nm and 120 nm in diameter, can target specific tissues to deliver molecular payloads, thus lending themselves as promising platform for cell-free therapies. In this study, sEVs were purified from the conditioned medium (CM) harvested from human bone marrow-derived MSC culture and purified using size-exclusion chromatography (SEC) or density gradient ultracentrifugation (DG-UC). Then sEVs were fully characterized for identity and integrity using multiple analytical methods, including single-particle, transcriptomic and proteomic analyses. Different in vitro cell-based assays were established to evaluate the biological effects of the purified sEVs. Specifically, scratch wound healing and tube formation assays using human umbilical vein endothelial cells (HUVECs) were used to evaluate the regenerative properties of MSC-sEVs. Our findings demonstrated that the in vitro functional properties of MSC-sEVs are correlated with sEVs’ purity levels obtained by different purification methods. Full article
(This article belongs to the Special Issue Exosomes—3rd Edition)
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23 pages, 6645 KB  
Article
Childhood Asthma Biomarkers Derived from Plasma and Saliva Exosomal miRNAs
by Abdelnaby Khalyfa, Mohit Verma, Meghan M. Alexander, Zhuanhong Qiao, Tammy Rood, Ragini Kapoor, Trupti Joshi, David Gozal and Benjamin D. Francisco
Int. J. Mol. Sci. 2025, 26(15), 7043; https://doi.org/10.3390/ijms26157043 - 22 Jul 2025
Cited by 2 | Viewed by 1343
Abstract
Asthma, the most common chronic respiratory condition in children, involves airway inflammation, hyper-responsiveness, and frequent exacerbation that worsen the airflow and inflammation. Exosomes, extracellular vesicles carrying microRNAs (miRNAs), play a key role in cell communication alongside other types of communication and are promising [...] Read more.
Asthma, the most common chronic respiratory condition in children, involves airway inflammation, hyper-responsiveness, and frequent exacerbation that worsen the airflow and inflammation. Exosomes, extracellular vesicles carrying microRNAs (miRNAs), play a key role in cell communication alongside other types of communication and are promising markers of asthma severity. This study compares exosomal miRNA and long non-coding RNA (lncRNA) profiles in boys with asthma, focusing on differences between those with normal lung functions and those with severe airflow obstruction. This study enrolled 20 boys aged 9–18 years with asthma, split into two groups based on their lung function. Ten had normal lung function (NLF; FEV1/FVC > 0.84, FEF75% > 69% predicted), while ten had severe airflow obstruction (SAO; FEV1/FVC < 0.70, FEF75 < 50% predicted). Saliva and blood samples were collected. Exosomes were isolated, quantified, and analyzed via small RNA sequencing to identify differentially expressed (DE) miRNA and lncRNA profiles. Bioinformatic tools were then used to explore potential miRNA biomarkers linked to asthma severity. SAO subjects were more likely to exhibit allergen sensitization, higher IgE levels, and more eosinophils. We identified 27 DE miRNAs in plasma and 40 DE miRNAs in saliva. Additionally, five key miRNAs were identified in both saliva and plasma which underline important pathways such as neurotrophins, T-cell receptor, and B-cell receptor signaling. We further outlined key features and functions of miRNAs and long non-coding RNAS (lncRNAs) and their interactions in children with asthma. This study identified DE miRNAs and lncRNAs in children with SAO when compared to those with NLF. Exosomal miRNAs show strong potential as non-invasive biomarkers for personalized asthma diagnosis, treatment, and monitoring. These RNA markers may also aid in tracking disease progression and response to therapy, thereby supporting the need for future studies aimed at applications in precision medicine. Full article
(This article belongs to the Special Issue Exosomes—3rd Edition)
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14 pages, 1651 KB  
Article
Extracellular Vesicle Abundance, but Not a High Aggregation-Prone Peptide Cargo, Is Associated with Dihydroartemisinin Exposure in Plasmodium falciparum
by Kwesi Z. Tandoh, Yunuen Avalos-Padilla, Prince Ameyaw, Elisabeth K. Laryea-Akrong, Gordon A. Awandare, Michael David Wilson, Neils B. Quashie, Xavier Fernàndez-Busquets and Nancy O. Duah-Quashie
Int. J. Mol. Sci. 2025, 26(9), 3962; https://doi.org/10.3390/ijms26093962 - 22 Apr 2025
Viewed by 1578
Abstract
Our understanding of the molecular mechanisms undergirding artemisinin (ART) resistance in Plasmodium falciparum is currently based on two organizing principles: reduced hemoglobin trafficking into the digestive food vacuole, resulting in lower levels of activated ART, and increased tolerance to ART-induced oxidative stress in [...] Read more.
Our understanding of the molecular mechanisms undergirding artemisinin (ART) resistance in Plasmodium falciparum is currently based on two organizing principles: reduced hemoglobin trafficking into the digestive food vacuole, resulting in lower levels of activated ART, and increased tolerance to ART-induced oxidative stress in the infected erythrocyte. We had previously proposed an extracellular vesicle (EV) export model of ART resistance in P. falciparum. This model predicts that EV abundance will be altered by ART exposure and that the peptide cargo of EVs from the ART-exposed condition will be enriched with aggregation-prone peptides. We tested the predictions of the EV export hypothesis in this study using in vitro culture assays of an ART-resistant transgenic line engineered on a 3D7 background (R561H) and a 3D7 knock-out line (PfVps60KO) with deficient EV production phenotype. EV enrichment was obtained from in vitro parasite culture supernatants via a series of ultracentrifugation and filtration steps, followed by size exclusion chromatography. A quality check on EVs was performed using dynamic light scattering. Liquid chromatography with tandem mass spectrometry was used to determine the proteome cargo from extracted EVs, and parasite peptides were queried for aggregation-prone tendency using open-access software. We report that dihydroartemisinin (DHA) exposure was positively correlated with EV abundance (coefficient estimate = 1038.58, confidence interval of 194.86–1882.30, and p-value = 0.018) and suggests that EV biogenesis is part of the parasite’s response to DHA/ART. Furthermore, our findings suggest the expression of a non-constitutive DHA-induced alternate EV biogenesis pathway as the PfVps60KO was observed to produce the highest number of EVs under DHA exposure. Finally, we show that EVs from both ART-susceptible and resistant parasites under DHA exposure carry a cargo of Chorein N-terminal domain-containing protein (PF3D7_1021700) with a high aggregation-prone index (prion-like domain [PrLD] score = 26.5) out of nine identified parasite peptides. The former of these findings is in concordance with the EV export hypothesis, which posits that the removal of DHA/ART-induced aggregated and/or misfolded peptides is critical to the parasite’s survival under DHA/ART exposure. This observation further implicates EVs in the development of the ART-resistant phenotype. However, the finding of one aggregation-prone peptide out of the nine parasite proteins in the EV cargo does not sufficiently support the EV export hypothesis. Future replicates of this study and further interrogations of the EV export hypothesis are needed. Full article
(This article belongs to the Special Issue Exosomes—3rd Edition)
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15 pages, 2167 KB  
Article
Small Extracellular Vesicles Derived from Cord Blood Plasma and Placental Mesenchymal Stem Cells Attenuate Acute Lung Injury Induced by Lipopolysaccharide (LPS)
by Ranga P. Thiruvenkataramani, Amal Abdul-Hafez, Tulasi Kesaraju, Hend Mohamed, Sherif Abdelfattah Ibrahim, Amira Othman, Hattan Arif, Ahmed A. Zarea, Mohammed Abdulmageed, Myrna Gonzalez Arellano, Tarek Mohamed, Masamitsu Kanada, Burra V. Madhukar and Said A. Omar
Int. J. Mol. Sci. 2025, 26(1), 75; https://doi.org/10.3390/ijms26010075 - 25 Dec 2024
Cited by 4 | Viewed by 3994
Abstract
Sepsis is a risk factor associated with increasing neonatal morbidity and mortality, acute lung injury, and chronic lung disease. While stem cell therapy has shown promise in alleviating acute lung injury, its effects are primarily exerted through paracrine mechanisms rather than local engraftment. [...] Read more.
Sepsis is a risk factor associated with increasing neonatal morbidity and mortality, acute lung injury, and chronic lung disease. While stem cell therapy has shown promise in alleviating acute lung injury, its effects are primarily exerted through paracrine mechanisms rather than local engraftment. Accumulating evidence suggests that these paracrine effects are mediated by mesenchymal stem cell (MSC)-derived small extracellular vesicles (sEVs), which play a critical role in immune system modulation and tissue regeneration. sEVs contain a diverse cargo of mRNA, miRNA, and proteins, contributing to their therapeutic potential. We hypothesize that sEVs derived from three distinct sources, cord blood plasma (CBP), Wharton jelly (WJ), and placental (PL) MSCs, may prevent the cytotoxicity induced by E. coli lipopolysaccharide (LPS) in lung alveolar epithelial cells. Objective: To determine the effects of CBP-, WJ-, and PL-MSCs-derived sEVs on cell viability, apoptosis, and proinflammatory cytokine production in alveolar epithelial cells and monocytes following LPS treatment. sEVs were collected from conditioned media of PL-MSCs, WJ-MSCs, and CBP using 50 nm membrane filters. sEVs were characterized based on nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), and Western blotting techniques. The protein concentration of isolated sEVs was used to standardize treatment doses. A549 cells and monocyte THP-1 cells were cultured and exposed to LPS in the presence or absence of sEVs for 72 h. Cell viability was measured using CellTiter-Glo 2.0 chemiluminescence-based assay. For cytokine analysis, A549 and THP-1 cells were pre-incubated for 24 h with or without PL- and CBP-sEVs, followed by exposure to LPS or control conditions for an additional 24 h. The conditioned media were collected, and interleukin-6 (IL-6) and interleukin-8 (IL-8) levels were quantified using ELISA. LPS treatment significantly reduced the viability of both A549 and THP-1 cells. The presence of CB- or WJ-sEVs significantly increased cell viability compared to controls. Cells treated with PL-sEVs showed increased cell viability but did not reach statistical significance. LPS-treated cells showed a significant increase in apoptosis and elevated levels of pro-inflammatory cytokines IL-6 and IL-8. All three sEVs types (CBP-, WJ-, and PL-sEVs) significantly reduced LPS-induced apoptosis and IL-6 release. Interestingly, while WJ-sEVs decreased IL-8, both CBP- and PL-sEVs led to an increase in IL-8 compared to their respective controls. CBP-, PL-, and WJ-derived sEVs demonstrated protective effects against LPS-induced injury in alveolar epithelial cells and monocytes, as evidenced by increased cell viability and modulation of pro-inflammatory cytokine release. These findings suggest that placenta-derived sEVs have the potential to modulate the immune response, mitigate inflammation, and prevent end-organ damage in neonatal sepsis. Full article
(This article belongs to the Special Issue Exosomes—3rd Edition)
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8 pages, 8360 KB  
Communication
Exosome Therapy: A Novel Approach for Enhancing Estrogen Levels in Perimenopause
by Samar Alkhrait, Mervat M. Omran, Mohammad Mousaei Ghasroldasht, Hang-Soo Park, Riham Katkhuda and Ayman Al-Hendy
Int. J. Mol. Sci. 2024, 25(13), 7075; https://doi.org/10.3390/ijms25137075 - 27 Jun 2024
Cited by 7 | Viewed by 3616
Abstract
Perimenopause significantly impacts women’s health globally, often managed with hormone replacement therapy (HRT) despite the associated risks. This study explores a novel alternative exosome therapy, aimed at stimulating estrogen production in ovarian tissues, thus offering a potential non-hormonal treatment for perimenopausal symptoms. Employing [...] Read more.
Perimenopause significantly impacts women’s health globally, often managed with hormone replacement therapy (HRT) despite the associated risks. This study explores a novel alternative exosome therapy, aimed at stimulating estrogen production in ovarian tissues, thus offering a potential non-hormonal treatment for perimenopausal symptoms. Employing ex vivo methodologies, ovarian cortex specimens from perimenopausal women were treated with exosomes derived from human umbilical cord mesenchymal stem cells and cultured under specific conditions (patent number: PCT/US2022/073467). The exosomes were produced under cyclic guanosine monophosphate (cGMP) conditions, ensuring high safety standards. Estrogen levels were quantified using enzyme-linked immunosorbent assay (ELISA), and gene expression changes in estrogen and follicle-stimulating hormone (FSH) receptors were assessed via quantitative polymerase chain reaction (PCR). Immunohistochemistry (IHC) was utilized to evaluate cellular proliferation and apoptotic markers. The results indicated a significant increase in estrogen levels and estrogen receptor-alpha (Erα) expression in treated tissues compared to controls. Additionally, a decrease in apoptotic markers and an increase in cellular proliferation markers were observed. These findings suggest that exosome therapy can effectively enhance estrogen production and modulate receptor sensitivity in perimenopausal ovarian tissues. This approach could serve as a safer alternative to HRT, aligning with the body’s natural regulatory mechanisms and potentially offering a more effective treatment option for managing perimenopausal symptoms. Full article
(This article belongs to the Special Issue Exosomes—3rd Edition)
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Review

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19 pages, 1678 KB  
Review
Role of Extracellular Vesicles in Abdominal Aortic Aneurysm: Pathophysiology, Biomarkers, and Therapeutic Potentials
by Kazuki Takahashi, Yusuke Yoshioka, Naoya Kuriyama, Shinsuke Kikuchi, Nobuyoshi Azuma and Takahiro Ochiya
Int. J. Mol. Sci. 2026, 27(2), 567; https://doi.org/10.3390/ijms27020567 - 6 Jan 2026
Viewed by 515
Abstract
Abdominal aortic aneurysm (AAA) is a life-threatening disease. Although AAA is generally asymptomatic, the mortality rate remains very high once rupture occurs, even with successful treatment. The pathophysiology of AAA involves inflammatory cell infiltration, smooth muscle cell apoptosis, and extracellular matrix degradation. However, [...] Read more.
Abdominal aortic aneurysm (AAA) is a life-threatening disease. Although AAA is generally asymptomatic, the mortality rate remains very high once rupture occurs, even with successful treatment. The pathophysiology of AAA involves inflammatory cell infiltration, smooth muscle cell apoptosis, and extracellular matrix degradation. However, there are various unclear aspects of pathophysiology due to cellular heterogeneity and multifactorial disease. Moreover, there are no blood biomarkers or available pharmacological drugs for AAA. Extracellular vesicles (EVs) are lipid bilayer particles released from every type of cell for intercellular communication. EVs include proteins, DNA, RNA (mRNA, microRNA), and lipids. EV cargos are delivered to recipient cells and modulate their biological effects. Although fewer studies have investigated EVs in AAA than in other cardiovascular diseases with similar molecular mechanisms, recent research indicates that EVs play a significant role in AAA development. Further research on EVs and AAA will contribute to the elucidation of AAA pathophysiology and the development of novel pharmacological drugs. In this review, we summarize the EV-associated pathophysiology, EV-based biomarkers, and EV-based treatment strategies in AAA. We also discuss the prospects for EVs research in AAA. Full article
(This article belongs to the Special Issue Exosomes—3rd Edition)
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28 pages, 1526 KB  
Review
Applications of Exosomes in Female Medicine: A Systematic Review of Molecular Biology, Diagnostic and Therapeutic Perspectives
by Heidi Mariadas, Jie-Hong Chen and Kuo-Hu Chen
Int. J. Mol. Sci. 2026, 27(1), 504; https://doi.org/10.3390/ijms27010504 - 3 Jan 2026
Cited by 1 | Viewed by 1320
Abstract
Exosomes are nanoscale extracellular vesicles that mediate intercellular communication by transporting microRNAs, proteins, and lipids. Generated through Endosomal Sorting Complex Required for Transport (ESCRT)-dependent mechanisms or ESCRT-independent pathways, exosomes are released when multivesicular bodies fuse with the plasma membrane. The ESCRT-dependent pathway involves [...] Read more.
Exosomes are nanoscale extracellular vesicles that mediate intercellular communication by transporting microRNAs, proteins, and lipids. Generated through Endosomal Sorting Complex Required for Transport (ESCRT)-dependent mechanisms or ESCRT-independent pathways, exosomes are released when multivesicular bodies fuse with the plasma membrane. The ESCRT-dependent pathway involves sequential protein complexes (ESCRT-0, I, II, III) that recognize and sort ubiquitinated cargo, induce membrane budding, and facilitate vesicle scission. In contrast, the ESCRT-independent pathway relies on membrane lipids such as ceramide and proteins like tetraspanins (CD9, CD63, CD81) to promote vesicle formation without ESCRT machinery. Furthermore, post-translational modifications, including ubiquitination, sumoylation, and phosphorylation, further serve as molecular switches, modulating the affinity of ESCRT complexes or cargo proteins for membrane domains and affecting ILV formation rates. In reproductive medicine, exosomes regulate oocyte maturation, embryo–endometrial crosstalk, placental development, and maternal–fetal communication. Altered exosomal signaling contributes to obstetric complications, including preeclampsia, gestational diabetes mellitus, and preterm birth, whereas distinct exosomal miRNA signatures serve as potential diagnostic biomarkers. In gynecology, dysregulated exosomes are implicated in endometriosis, polycystic ovary syndrome, premature ovarian insufficiency, and gynecological malignancies. In contrast, mesenchymal stem cell-derived exosomes show therapeutic promise in restoring ovarian function and enhancing fertility outcomes. The distinctive molecular profiles of circulating exosomes enable minimally invasive diagnosis, while their biocompatibility and ability to cross biological barriers position them as vehicles for targeted drug delivery. Characterization of accessible data provides non-invasive opportunities for disease monitoring. However, clinical translation faces challenges, including standardization of isolation protocols, establishment of reference ranges for biomarkers, and optimization of therapeutic dosing. This review summarizes exosome biogenesis, characterization methods, physiological functions, and clinical applications in obstetrics and gynecology, with an emphasis on their diagnostic and therapeutic potential. Future directions include large-scale biomarker validation studies, engineering approaches to enhance exosome targeting, and integration with precision medicine platforms to advance personalized reproductive healthcare. Full article
(This article belongs to the Special Issue Exosomes—3rd Edition)
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11 pages, 1331 KB  
Review
Exosomes in Breast Milk: Their Impact on the Intestinal Microbiota of the Newborn and Therapeutic Perspectives for High-Risk Neonates
by Delia Cristóbal-Cañadas, Rocio Parrón-Carrillo and Tesifón Parrón-Carreño
Int. J. Mol. Sci. 2025, 26(7), 3421; https://doi.org/10.3390/ijms26073421 - 5 Apr 2025
Cited by 4 | Viewed by 3499
Abstract
Breast milk exosomes are essential for the nutrition and immune development of the newborn. These 30–150 nm extracellular vesicles contain microRNAs (miRNAs), mesessenger RNAS (mRNA)s, proteins and lipids that facilitate cellular communication and modulate the neonatal immune system. In this article, we analyse [...] Read more.
Breast milk exosomes are essential for the nutrition and immune development of the newborn. These 30–150 nm extracellular vesicles contain microRNAs (miRNAs), mesessenger RNAS (mRNA)s, proteins and lipids that facilitate cellular communication and modulate the neonatal immune system. In this article, we analyse the impact of breast milk exosomes on the intestinal microbiota of the newborn, especially in high-risk neonates such as preterm infants or neonates at risk of necrotising enterocolitis (NEC). Exosomes promote the colonisation of beneficial bacteria such as Bifidobacterium and Lactobacillus and strengthen the intestinal barrier. They also regulate the immune response, balancing defence against pathogens and tolerance to non-pathogenic antigens. This effect is key for high-risk infants, who benefit from their anti-inflammatory and preventive properties against complications such as NEC. Research points to their potential therapeutic uses in neonatal care, opening up new opportunities to improve the health of vulnerable newborns through the protective effects of breast milk exosomes. Full article
(This article belongs to the Special Issue Exosomes—3rd Edition)
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