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The extracellular space contains RNAs both inside and outside extracellular vesicles (EVs). Among RNA types, tRNAs and tRNA-derived small RNAs (tDRs) tend to be abundant and are frequently detected when performing small RNA sequencing of extracellular samples. For several applications, including answering basic biology questions and biomarker discovery, it is important to understand which specific extracellular tRNAs and tDRs are inside EVs and which are not. We have observed that EVs contain mainly full-length tRNAs, while cells also release full-length tRNAs into nonvesicular fractions. However, these nonvesicular tRNAs are fragmented by extracellular ribonucleases into nicked tRNAs, which can dissociate into tDRs both in extracellular samples and in the laboratory. It is therefore crucial to separate EVs from other nonvesicular RNA-containing extracellular carriers to prevent cross-contamination. Otherwise, extracellular tDR profiling may mix up signals coming from structurally and functionally different carrier types. Here, we provide two protocols that achieve this by: (a) density gradient separation and, (b) the use of commercial, pre-packed size-exclusion chromatography columns. The first protocol is time-consuming but achieves high resolution, while the second protocol is faster, simpler, and recommended for routine separations. Taken together, they form a solid experimental toolkit for addressing different questions related to extracellular tRNA biology or biomarker discovery.
Kidney transplant monitoring and early identification of graft dysfunction are central needs for long-term graft survival. Although kidney biopsy represents the gold standard in diagnostic procedures, its invasiveness may limit frequent longitudinal evaluation, highlighting the necessity of non-invasive diagnostic tools. Urine has emerged over the years as an easily obtainable source of cellular and molecular components derived from transplanted kidneys. Particularly, exfoliated cells and extracellular vesicles (EVs) represent complementary and interconnected markers able to reflect tissue injury, inflammatory signals, immune cell infiltration, and regenerative processes occurring in the graft. Also, recent advances in transcriptomics, proteomics, metabolomics, and single-cell technologies have expanded the diagnostic and mechanistic value of urinary liquid biopsy, enabling the identification of disease-specific molecular signatures associated with rejection, delayed graft function, fibrosis, and graft loss. This review discusses the emerging concept of an integrated urinary cell-EV ecosystem and highlights how integrated multi-omic approaches may transform non-invasive graft surveillance and advance precision medicine in kidney transplantation.
Bacterial extracellular vesicles (BEVs) are increasingly proposed as materials for skin-directed cosmetics, yet rapid adoption of "exosome" terminology has outpaced clarity on their origin, composition, and manufacturing quality. This review argues that the value of BEVs depends on scientific discipline rather than marketing appeal, and that they are promising because they are biologically potent, not because they are intrinsically benign. We retain BEVs as the scientific umbrella term for vesicles released by bacteria and we propose the term microbiome-derived vesicles (MDVs) as the consumer-facing designation for qualified commensal BEVs - a surface term that avoids the difficulty of "bacterial" while its definition preserves bacterial provenance. We develop a three-axis framework for BEV identity that integrates compositional analysis, producer-strain genomics, and functional or safety profiling, and we position whole-genome sequencing (WGS) as decisive for source qualification and mechanistic interpretation but insufficient to prove the efficacy of a purified preparation. Building on this framework, we summarize isolation, purification, and analytical characterization requirements; interpret current skin-efficacy evidence in light of its methodological limits; and discuss formulation, cosmetic application, regulatory positioning, and manufacturable quality. We conclude that transparent bacterial provenance, reproducible preparation, and evidence proportionate to the claims made are prerequisites for evaluating commensal BEVs, described for skin applications as MDVs, as a scientifically defined cosmetic platform.
Glycylprolyl dipeptidase activity was measured in cells, extracellular vesicles (ECV) and the soluble extracellular protein fraction (EP) of batch cultures of strains W50 and W50/BEI. Total culture enzyme activity of W50 dropped with age whilst that of W50/BEI remained constant. Activity was highest in the cellular fraction, greater for W50/BEI than W50 and rose with culture age. Both strains showed similar ECV activities but these declined with culture age. The EP glycylprolyl dipeptidase activity of W50/BEI in older cultures rose to a level 13-fold greater than W50. The majority of extracellular activity was represented by the ECV for strain W50 but by EP for W50/BEI. Variable but incomplete attenuation of activity was achieved by dithiothreitol. ECV and EP activities were associated with a high molecular mass fraction, but a smaller fraction (molecular mass 30,000) was detected in W50/BEI EP.
The ability of Porphyromonas gingivalis to acquire iron in the iron-limited environment of the host is crucial to the colonization of this organism. We report here on the isolation and characterization of a transpositional insertion mutant of P. gingivalis A7436 (designated MSM-3) which is defective in the utilization and transport of hemin. P. gingivalis MSM-3 was selected on the basis of its nonpigmented phenotype on anaerobic blood agar following mutagenesis with the Bacteroides fragilis transposon Tn4351. P. gingivalis MSM-3 grew poorly when supplied with hemin as a sole source of iron; however, growth was observed with hemoglobin or inorganic iron. P. gingivalis MSM-3 grown in either hemin-replete or hemin-depleted conditions bound and transported less [14C]hemin or [59Fe]hemin than did the parent strain. At 4 h, P. gingivalis MSM-3 grown in hemin-replete conditions transported only 10,000 pmol of hemin per mg of protein, or 14% of the amount transported by P. gingivalis A7436. Unlike P. gingivalis A7436, hemin binding and transport by P. gingivalis MSM-3 were not tightly regulated by hemin or iron. Examination of P. gingivalis MSM-3 cultures by electron microscopy revealed an overproduction of membrane vesicles, and determination of the dry weight of purified vesicles indicated that P. gingivalis MSM-3 produced twice as much membrane vesicles as did strain A7436. Extracellular vesicles isolated from P. gingivalis MSM-3 also were found to express increased hemolytic and trypsin-like protease activities compared with the parent strain. When inoculated into subcutaneous chambers implanted in mice, P. gingivalis MSM-3 was highly infectious and more invasive than the parent strain, as indicated by secondary lesion formation and death. Taken together, these results indicate that the decreased transport of hemin by P. gingivalis MSM-3 results in the increased expression of several virulence factors which may be coordinately regulated by hemin.
Highly purified preparations of human basophils have been studied ultrastructurally to delineate quantifiably those alterations associated with immunologically-induced histamine release. Of six characteristic variations of basophil morphology, totally degranulated cells, those with some exteriorized granules and those with some extracellular vesicles were almost exclusively associated with antigen challenge. Of these, total degranulation without extracellular granules or vesicles was most frequent. A correlation was found between percentage histamine released and percentage totally degranulated cells present in the samples incubated with antigen. In addition, increased plasma membrane folding and irregularity were more prevalent in stimulated samples than in controls and their mean frequency was related quantifiably to the percentage of histamine released in each group. Cells with empty vesicles or electronlucent intracellular granules or both occurred to the same extent in experimental and control aliquots. The possible of histamine release is discussed.
BACKGROUND: People spend the majority of their lives indoors, yet the risk and virulence potential of household microbiota remain largely unexplored, particularly in developing countries. RESULTS: Here, we conducted a nationwide survey on both dust samples and health information across 118 Chinese households. The microbiota composition and its functional units were analyzed using absolute 16S rRNA/ITS sequencing, metagenomics, and metaproteomics. Cross-domain network analysis of the core microbial communities revealed robust co-occurrence patterns in household dust. The mean absolute abundance of potentially pathogenic bacteria and fungi in households was 2.39 × 105 and 2.83 × 106 DNA copies/g dust. The potentially pathogenic community was primarily influenced by latitude, relative humidity, and average temperature. Although total absolute abundance was substantially lower in urban areas, the relative abundance of potentially pathogenic bacteria was markedly higher compared to rural environments. While urban-rural differences existed, the underlying statistical drivers were the environmental variables. The absolute abundance of potential pathogens was significantly associated with the prevalence of rhinitis, wheeze, and dermatitis in 266 participants. Children were identified as the highest-risk group from inhalation exposure of average daily dose. A total of 170 bacterial, 223 fungal virulence factors (VFs), and 370 antibiotic resistance genes (ARGs) were detected in dust and dust extracellular vesicle (EV)-associated DNA. EV-associated cargoes contributed 47.13% to the bacterial VF profiles, 11.90% to fungal VF profiles, and 44.45% to ARG profiles. Metaproteomic analysis confirmed the presence of VF profiles in dust EVs, which was further verified by curated proteomics data from 35 household pathogens. CONCLUSIONS: This study provides a comprehensive, quantitative framework linking indoor microbial exposure to health risks, highlighting EVs as a non-negligible, novel, extracellular mechanistic pathway for health impact in household environments. Video Abstract.
Cancer progression is systemically influenced by distant organ dysfunction induced by primary tumors, yet how long-distance tumor-organ crosstalk regulates antitumor immunity remains unclear. Here, we identify host metadherin (MTDH) as a critical regulator of tumor-induced immunosuppression and metabolic reprogramming via tumor-liver interactions. Using Mtdh knockout mouse models, we show that concurrent MTDH loss in hepatocytes and CD8+ T cells enhances effector T cell function and suppresses tumor growth and metastasis. Mechanistically, tumor-derived extracellular vesicles and particles (EVPs) activate Kupffer cells to secrete tumor necrosis factor α (TNF-α) and TGF-β, which suppress hepatic PPARα-mediated lipid oxidation via nuclear factor κB (NF-κB) signaling. MTDH loss restores hepatic lipid catabolism, reduces systemic lipid levels, and promotes mitochondrial metabolic reprogramming in CD8+ T cells under lipid-reduced conditions, thereby boosting antitumor immunity. Genetic or pharmacological targeting of MTDH synergizes with anti-PD-1 therapy. These findings establish host MTDH as a key mediator of tumor-liver crosstalk through metabolic and immune interactions, driving systemic cancer progression.
BACKGROUND: Insulin resistance (IR) is implicated in central nervous system disorders, including depression and Alzheimer's disease (AD). METHODS: We analyzed biological samples from two cohorts of clinical trial participants: (1) participants with unremitted depression after six months of treatment as usual who received pioglitazone (PPARγ agonist, N = 12) or placebo and (2) middle-aged participants at genetic risk for AD who received liraglutide (glucagon-like peptide 1 [GLP1] receptor agonist, N = 15) or placebo. These cohorts, which previously showed treatment-related improvements in peripheral IR, were used to assess the effects of pioglitazone and liraglutide on CNS insulin signaling using neuron-derived extracellular vesicles (NDEVs) as biomarkers. We utilized biological samples to measure biomarkers of IR in NDEVs. Eleven Akt-mTOR pathway proteins were measured before and after 12 weeks of treatment in both groups. RESULTS: Participants who received pioglitazone experienced broader changes, with significant increases in GSK3β (Ser9), mTOR (Ser2448), and RPS6 (Ser235/Ser236; all P ≤ .02) compared with placebo, and 77% of participants showed mTOR (Ser2448) response. Participants who received liraglutide demonstrated significantly increased NDEV-associated phosphorylated Akt (Ser473) and mTOR (Ser2448; P = .04 and P = .025, respectively) compared with placebo, with 40% and 30% of participants in the liraglutide group showing biomarker response in both Akt (Ser473) and mTOR (Ser2448), respectively. These effects appeared relatively independent from changes in fasting plasma insulin and glucose concentration at 120-minutes during the oral glucose tolerance test. DISCUSSION: Our findings demonstrate CNS-specific biomarker responses to both PPARγ agonists and GLP1 receptor agonists.
Melioidosis, caused by Burkholderia pseudomallei (Bp), is a life-threatening disease characterized by diverse clinical manifestations and limited diagnostic capabilities. Extracellular vesicles (EVs) have emerged as critical carriers of novel antibody targets for serodiagnosis. In this study, we established a Bp-infected BEAS-2B cell model (Bp/BEAS-2B) and isolated EV from both Bp and Bp/BEAS-2B cells to generate EV proteome, identifying potential antigenic biomarkers for melioidosis diagnosis. Bioinformatics analysis identified PPEP and POMCR proteins as candidate antigens, with BLF1 and omp A serving as positive controls. Using a self-developed IgM-ELISA, serum samples from 43 melioidosis patients and 47 healthy volunteers were analyzed to detect antibodies against these antigens. Anti-POMCR IgM demonstrated exceptional diagnostic performance, with an AUC of 0.9872 (95% CI: 0.9713-1.003), sensitivity of 93.02% and specificity of 97.92% at a cutoff value of OD450 = 0.118. Similarly, IgM against PPEP, BLF1, and omp A also showed high diagnostic accuracy, with AUC values of 0.969, 0.9621, and 0.976, respectively. The accuracy of anti-POMCR and anti-PPEP were 96.43% and 95.54%, respectively, equivalent to anti-omp A (93.75%) and anti-BLF1 (91.96%). Antibodies to EV-derived proteins effectively differentiated melioidosis patients from other bacterial infections and healthy volunteers, highlighting their clinical potential as diagnostic tools for melioidosis.
The sensing of Gram-negative Extracellular Vesicles (EVs) by the innate immune system has been extensively studied in the past decade. In contrast, recognition of Gram-positive EVs by innate immune cells remains poorly understood. Comparative genome-wide transcriptional analysis in human monocytes uncovered that S. pyogenes EVs induce proinflammatory signatures that are markedly distinct from those of their parental cells. Among the 209 genes exclusively upregulated by EVs, caspase-5 prompted us to study inflammasome signaling pathways in depth. We show that lipoteichoic acid (LTA), a structural component of Gram-positive bacterial membranes present on EVs from S. pyogenes and other Gram-positive species, is sensed by TLR2 which triggers the alternative inflammasome composed of NLRP3 and the inflammatory caspases-4/-5 to mount an IL-1β response without inducing cell death. For S. pyogenes, we identify TLR8 as a sensor to mediate caspase-4/-5-dependent IL-1β secretion. Notably, inflammasome activation by intact bacteria is independent of the global virulence regulator CovS in monocytes. Overall, our study highlights a new role for TLR2 and caspase-4/-5 in the recognition of Gram-positive EVs in human monocytes.
Cancer-derived extracellular vesicle (EV) nanoparticles carry important biomarkers but are difficult to recover from plasma, making EV-based diagnostics a challenge for clinical settings. Here, we demonstrate nanoparticle-based detection of pancreatic cancer using dielectrophoresis (DEP) nanoparticle recovery technology, which purifies nanoparticles from undiluted plasma and quantifies associated biomarkers. We combined both nanoparticle recovery and biomarker quantification on a single device by simultaneously collecting cell-free DNA nanoparticles and EVs followed by on-chip biomarker fluorescent staining for DNA and Glypican-1. Using a blinded cohort, these biomarkers differentiated pancreatic cancer from benign pancreatic diseases, including cysts, pancreatitis, and precancerous low-grade intraductal papillary mucinous neoplasm (IPMN) lesions, with a sensitivity of 0.92, a specificity of 0.83, and an AUC of 0.93. The AUC increased to 0.97 for patients over 50 years old. This is higher than the standard invasive endoscopic ultrasound-guided fine needle aspiration tissue biopsy procedure (AUC 0.79). This study is among the first demonstrating a combined threshold of DNA and protein levels that can distinguish pancreatic cancer from its precursor IPMN lesions. We also demonstrated the detection of early-stage pancreatic cancer and high-grade in situ precancerous lesions. This DEP-based technique shows that multiple types of cancer-derived nanoparticles can be quickly and easily recovered from plasma making it promising for future clinical diagnostics.
Arterial disease management is shifting from antiproliferative drug-eluting stents toward approaches that restore endothelial function and modulate smooth muscle cell (SMC) behavior. Stem cell-derived extracellular vesicles (EVs) carry miRNAs that promote endothelial proliferation and migration while restraining aberrant SMC growth and inflammation. Here, human induced pluripotent stem cell (iPSC)-derived EVs were collected by ultracentrifugation and incorporated into 50:50 poly (lactic-co-glycolic acid) (PLGA 503) core-shell nanofibrous membranes, which were fabricated as stent coatings for sustained release to overcome rapid clearance and poor tissue retention. EVs derived from three independent iPSC lines all enhanced tube formation in human umbilical vein endothelial cells (HUVECs) under hypoxic and serum-starved conditions and revealed a trend toward reduced platelet-derived growth factor-BB (PDGF-BB)-induced smooth muscle cell (SMC) migration. The fabricated core-shell nanofibers enabled sustained EV release, maintaining therapeutic efficacy for 28 days. Small RNA sequencing (NGS) analysis demonstrated that EVs from these independent iPSC lines shared miR-148a-3p and members of the miR-92 family, which collectively accounted for more than 75% of the reads within the 25 top-expressed miRNA set. In vitro, iPSC-EVs enhanced HUVEC proliferation and survival signaling by downregulating the negative regulators ERRFI1 and VHL, which are specific targets of miR-148a-3p and the miR-92 family, thereby activating the EGFR and HIF-1α axes and driving downstream ERK1/2 and VEGF expression under hypoxic and serum starvation stress conditions. Concurrently, iPSC-EVs prevented PDGF-BB-induced SMC phenotypic switching by downregulating ROCK1, a target of miR-148a-3p, thereby inhibiting downstream AKT and ERK signaling and preserving contractile markers while suppressing the synthetic phenotype. In vivo, the iPSC-EV-functionalized scaffolds significantly accelerated re-endothelialization and inhibited neointimal hyperplasia, evidenced by the upregulation of angiogenic factors (VEGF, CD31) and the concurrent suppression of pathological remodeling markers (α-SMA, MMPs) and inflammatory cytokines (IL-6, TGF-β1). Therefore, iPSC-EVs enriched with specific miRNAs and delivered via PLGA 503 core-shell nanofibers promote endothelial repair while suppressing SMC overgrowth, providing a promising strategy for vascular healing.
Porphyromonas gingivalis, an important pathogen in periodontitis, produces extracellular vesicles that aggregate with Actinomyces viscosus cells. A 40-kDa outer membrane protein (OMP)-coding gene from P. gingivalis was cloned and the protein was found to be localized in these vesicles. The recombinant 40-kDa OMP did not show aggregation activity. However, affinity-purified antibody against the recombinant protein significantly inhibited aggregation of P. gingivalis vesicles with A. viscosus cells. The antibody also inhibited cellular coaggregation of several strains of P. gingivalis with A. viscosus cells, but not with other periodontal pathogens. Moreover, aggregation of A. viscosus cells with P. gingivalis vesicles was inhibited in a dose-dependent manner by pre-treatment of the A. viscosus cells with the recombinant protein. These findings suggest that the 40-kDa OMP may be an important aggregation factor of P. gingivalis.
The mechanisms by which macromolecules are transported through the cell wall of fungi are not known. A central question in the biology of Cryptococcus neoformans, the causative agent of cryptococcosis, is the mechanism by which capsular polysaccharide synthesized inside the cell is exported to the extracellular environment for capsule assembly and release. We demonstrate that C. neoformans produces extracellular vesicles during in vitro growth and animal infection. Vesicular compartments, which are transferred to the extracellular space by cell wall passage, contain glucuronoxylomannan (GXM), a component of the cryptococcal capsule, and key lipids, such as glucosylceramide and sterols. A correlation between GXM-containing vesicles and capsule expression was observed. The results imply a novel mechanism for the release of the major virulence factor of C. neoformans whereby polysaccharide packaged in lipid vesicles crosses the cell wall and the capsule network to reach the extracellular environment.
Borrelia burgdorferi produces extracellular vesicles containing various borrelial protein antigens when propagated in vitro in culture media. Commonly observed components of borrelial vesicle preparations are borrelial surface antigens, bovine serum albumin, and the heavy chains of rabbit immunoglobulin G and immunoglobulin M. This study employed ultracentrifugation to harvest borrelial vesicles and analyzed these preparations by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western immunoblotting. We demonstrated that the rabbit mu heavy-chain band observed was devoid of OspA or at most levels below those detectable by immunoblot. We also demonstrated the recovery of borrelial vesicles at relative centrifugal forces as low as 25,000 x g, compared with the force of > 200,000 x g normally employed. Further, the mu heavy-chain band was recovered from uninoculated growth media processed at 25,000 x g, suggesting that it behaves as a particle rather than as a soluble molecule under these conditions. Lastly, vesicles were demonstrated to be present in preparations harvested from growth media supplemented with fetal calf serum, suggesting that vesicle production by B. burgdorferi can occur in the absence of immunoglobulins.
Matrix vesicles (MV) are microstructures localized to the extracellular matrix of developing hard tissues that induce mineral formation. MV proteins are not well characterized, and little is known of how they interact with the surrounding matrix. However, recent electron microscopic studies indicate that MV interact with matrix proteins in growth plate cartilage. In the studies now reported, procedures developed for dissecting various components from isolated MV led to the discovery that two major vesicle proteins (38 and 46 kDa) are readily released from MV by low ionic strength solutions. These low ionic strength-soluble proteins (LISSP) were shown to be major fragments of the link protein (LP) and hyaluronic acid-binding region (HABR) of matrix proteoglycans: they react immunologically with highly specific monoclonal antibodies to LP and HABR, and the NH2-terminal sequence of the 38-kDa LISSP is essentially identical to residues 40-78 of chicken cartilage LP and that the 46-kDa LISSP represents HABR. Release of both LISSP is enhanced by hyaluronidase treatment, indicating anchorage by a hyaluronate-mediated mechanism. Both LP and HABR are firmly attached to MV in either isotonic or hypertonic solutions. In contrast, our other studies show that dissociation of type II collagen from MV occurs only with hypertonic salts which do not release the LISSP. Thus, strong interactions occur under physiological conditions between MV and both the proteoglycans and collagens, but these take place by different mechanisms.