Search Results (739)

Background: Lymph node metastasis (LNM) is a determinant of prognosis and in guiding chemotherapy decisions in breast cancer. Herein, we aimed to discover the protease content of the circulating large extracellular vesicles (L-EVs) as potential markers for LNM. Methods: L-EVs were isolated from the plasma of chemotherapy-naïve breast cancer patients with negative LNM (nLNM, n = 40) and positive LNM (pLNM, n = 32) patients using differential centrifugation. The isolated L-EVs were characterized by Transmission Electron Microscopy, dynamic light scattering and EV marker profiling, and their protease content was profiled using unbiased proteome profiler human protease array. Results: Protease profiling uncovered that L-EVs contained significantly elevated levels of MMP-8 (p < 0.001) and MMP-9 (p < 0.05) in pLNM versus nLNM patients. Further validation by Western blotting confirmed that latent MMP-8 was significantly increased (p < 0.01) in L-EVs from pLNM patients. Interestingly, zymography revealed that L-EVs isolated from pLNM patients contained higher levels of latent MMP-9 compared with those from nLNM patients, whereas gelatinolytically active MMP-2 was only detected in L-EVs from pLNM patients and not in those from nLNM. Online datasets revealed that higher MMP-8 and MMP-9 mRNA levels were associated with poorer overall, relapse-free, and distant metastasis-free survival. Receiver operating characteristic (ROC) plotter analyses indicated that MMP-2 and MMP-8 may serve as predictive biomarkers for response to specific chemotherapeutic regimens. Conclusions: These findings highlight the potential clinical utility of L-EV-derived MMP-2, MMP-8, and MMP-9 expressions and/or activities, as non-invasive blood-based markers associated with nodal progression and therapeutic response. Full article

Extracellular vesicles (EVs) can disseminate replication-competent viral genomes complexed with selected host proteins, enabling stealth cell-to-cell transfer within lipid membrane-enclosed bubbles. In addition to complementing free-virion spread, EV-associated genomes can be protected from neutralizing antibodies and persist under conditions in which classical virion production decreases. Here, we propose a route-resolved framework in which interconnected cellular secretory pathways, including endoplasmic reticulum (ER) remodeling, multivesicular body (MVB) biogenesis, secretory autophagy, and plasma-membrane budding, jointly generate EV heterogeneity and create discrete opportunities for the capture, protection, and export of infectious cargo. We highlight reticulon-3 (RTN3), an ER-shaping protein, as an upstream regulator that can couple infection-induced ER microdomains to endosomal docking and to autophagy-linked trafficking decisions that bias intermediates toward secretion rather than degradation. Supporting this view, transmission electron microscopy of dengue virus-infected cells reveals extensive vesicular remodeling, including irregular MVBs adjacent to the plasma membrane and autophagosome-like double-membrane structures, consistent with altered vesicular routing following RTN3 perturbation. Collectively, these route-resolved, spatially organized spatio-organelle changes support a pathomechanistic model in which RTN3-mediated ER remodeling reshapes ER-endosome-autophagy trafficking interfaces, creating regulated decision points that can be leveraged to stratify infectious EV subsets (with infectivity-linked single-vesicle and quantitative proteomics approaches) and to inform host-directed strategies that curb non-lytic viral dissemination. Full article

Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly recognized as a systemic disorder shaped by genetic variants and network-level interactions beyond obesity and insulin resistance. This study aimed to define the genetic and proteomic architecture of MASLD by integrating GWAS and plasma proteomic profiling from the UK Biobank. Genome-wide association analyses were conducted under additive and dominant models, with functional annotations performed using SIFT, PolyPhen-2, PROVEAN, REVEL, CADD, MutationTaster, and conservation metrics (GERP++, phyloP, phastCons, and B-statistic). Differential protein expression was assessed using the Olink^® platform, and STRING was applied for protein–protein interaction analysis. MASLD patients showed male predominance and significant differences in hepatic (AST, ALT, GGT, PDFF), metabolic (glucose, triglycerides, TyG index), and inflammatory markers (CRP, neutrophils, NLR, CAR). GWAS confirmed PNPLA3 (rs738409, I148M) and TM6SF2 (rs58542926, E167K) as major risk variants, while SAMM50 and NCAN showed weaker but conserved associations. Proteomics revealed downregulation of IGFBP2, IGFBP1, PON3, CKB, and APOF and upregulation of CPM, IGSF9, GUSB, ACY1, AFM, LEP, and GSTA1/3. PPI analysis identified ADIPOQ, LEP, FGF21, and ADH1B as central hubs in metabolic and inflammatory regulation. MASLD should be regarded as a network disease involving lipid metabolism, insulin/IGF signaling, mitochondrial function, and ECM–inflammatory pathways. These findings highlight PNPLA3 and TM6SF2 as major genetic drivers, while SAMM50, NCAN, and peripheral proteins contribute regulatory roles, suggesting novel biomarkers and therapeutic targets. Full article

Postprandial variability in glucose and protein levels is one of the elements of insulin resistance (IR) and prediabetes, which is an area precursor to type 2 diabetes mellitus (DM). The objective of the study was a comprehensive proteomic analysis according to glucose tolerance in the general population who did not self-report DM or other diseases. We used Olink^® Reveal, a novel, high-throughput platform by Olink Proteomics based on their Proximity Extension Assay (PEA), to identify levels of 1034 circulating proteins in small volumes (4 µL) of plasma samples. The study enrolled 508 participants (mean age 52 ± 10.5 years, 47.2% men) from the population-based study, Bialystok PLUS Polish Longitudinal University Study. The study population was categorized according to glucose metabolism in comparison to impaired fasting blood glucose (IFG), impaired glucose tolerance (IGT), and newly diagnosed DM. Analysis of variance (ANOVA) adjusted for age, weight, fat mass, lean mass, and body mass index (BMI), identified 19 proteins significantly associated with categories of glucose tolerance. Of the five markers with the greatest ability to distinguish newly diagnosed diabetes from non-diabetic participants, paralemmin 2 performed best (AUC = 0.81; 77% sensitivity, 75% specificity), whereas furin was the most accurate for detecting any abnormal glucose regulation (AUC = 0.69). A linear regression model adjusted for the same confounding factors showed statistically significant associations between Hb_A1c levels and 37 proteins. Our findings highlight multiple proteins with significantly different levels across categories of glucose tolerance, especially between the healthy controls and the group with newly diagnosed DM. The consistent patterns of protein level differences, independent of body composition, suggest potential involvement in the progression of glucose metabolism disturbances and provide unique insights into pathomechanisms. These findings identify PALM2, FURIN, PDZK1, ACAA1, and IL18R1 as potential biomarkers of early dysglycemia. Full article

Background/Objectives It is known that failure to gain sufficient bone during skeletal growth and maturation phases predisposes to the development of senile osteoporosis as age-related bone loss ensues. There is limited knowledge about factors that are necessary for the pubertal growth spurt and achievement of peak bone mass. Diminution or disappearance of Juvenile Protective Factors (JPFs) after a given maturational stage could contribute to the onset of age-related declines in a variety of physiological functions, including bone physiology. Methods With available pediatric platelet-poor plasma (PPP) and mesenchymal/skeletal stem cells (MSCs), we tested whether proteomics and RNA-seq methodology have potential for the discovery of novel regulators of pubertal skeletal growth. Results Our data demonstrate that pediatric PPP rejuvenates age-related compromised MSC functions; that Mass Spectrometry (MS)-based proteomics identified known and novel circulating tissue growth/trophic factors in human PPP of pubertal, as compared with pre-pubertal, and post-pubertal subjects; and that the unbiased RNA-Seq approach revealed new genes and networks of genes that are dramatically elevated or diminished in pubertal MSCs. Conclusions The findings support the hypothesis that the characterization of pro-osteogenic JPFs could lead to the identification of novel therapeutic approaches to promote bone health in the elderly and of potential treatment regimens for senile osteoporosis. Full article

Background/Objectives: CDKL5 deficiency disorder (CDD) is a rare X-linked developmental and epileptic encephalopathy characterized by early onset refractory epilepsy and severe neurodevelopmental impairment with autistic features. Despite advances in genetic diagnosis, objective biomarkers reflecting disease mechanisms remain limited. Extracellular vesicles (EVs) circulating in the blood may contain disease-related proteins derived from the central nervous system. This study aimed to characterize the plasma EV proteome in CDD in a hypothesis-generating exploratory framework and identify the candidate molecular pathways associated with this disorder. Methods: Plasma samples from seven patients with genetically confirmed CDD and seven neurotypical developmental controls were analyzed. Extracellular vesicle-containing preparations (EVs-cp) were isolated via immunoprecipitation using antibodies against CD9, CD63, and CD81. Proteomic profiling was performed using data-independent mass spectrometry. Differentially expressed proteins were identified using Welch’s t-test with a false discovery rate correction. Functional enrichment, protein interaction network, and correlation analyses were performed using CDKL5 Clinical Severity Assessment (CCSA) scores. Results: In total, 5617 proteins were identified, of which 3510 were used for quantitative analysis. Compared to the controls, 2108 proteins were upregulated and 158 were downregulated in the CDD samples. Enrichment analysis revealed alterations in vesicle-mediated transport, cytoskeletal organization, and immune-related pathways. Several proteins were also correlated with clinical severity scores. Conclusions: Plasma EV proteomics revealed molecular alterations associated with CDD and provided a potential approach for biomarker discovery and mechanistic investigation. Full article

To address cryodamage in Culter alburnus sperm, this study evaluated the effects of trehalose supplementation in a conventional cryomedium (D-15 + 10% ethylene glycol). Six experimental groups were established: fresh sperm (G1), a conventional cryomedium (G2), groups supplemented with 10, 100, or 200 mmol/L trehalose (G3–G5), and a control group with extender only (G6). The group with 100 mmol/L trehalose (G4) was associated with improved post-thaw motility parameters (activation rate, movement time, and lifespan) and higher antioxidant (superoxide dismutase and catalase) and energy metabolism (ATPase, succinate dehydrogenase, lactate dehydrogenase) enzyme activities. Ultrastructural damage in G4 included partial plasma membrane rupture and mitochondrial swelling, while G6 exhibited additional damage features including membrane disintegration, mitochondrial disruption, and flagellar fracture. Proteomic analysis revealed that, compared to G1, G4 exhibited higher abundance of proteins (e.g., Histone H2A, cytochrome c oxidase, profilin) involved in structural integrity and energy homeostasis, whereas G6 showed signatures of oxidative stress and metabolic dysfunction (lower abundance of NADH dehydrogenase and higher abundance of calcium-transporting ATPase and glutathione S-transferase). In conclusion, 100 mmol/L trehalose was associated with improved cryopreservation outcomes, and the proteins identified provide a basis for further investigation. This approach offers a framework for refining germplasm conservation strategies in aquaculture. Full article

Background/Objectives: Determining the cardiovascular cause of death, particularly distinguishing ischemic from congestive mechanisms, remains challenging in forensic practice, especially in early ischemia without definitive histological findings. Proteomic techniques and molecular profiling may provide complementary diagnostic information beyond conventional autopsy. Methods: We applied an untargeted high-resolution proteomic approach to postmortem cardiac tissue samples from cardiovascular (ischemic and congestive) and non-cardiovascular deaths. Identified proteins were analyzed using bioinformatic and differential expression workflows. Selected candidates were evaluated in peripheral blood samples for translational validation using statistical modeling, including regression analyses and receiver operating characteristic (ROC) curve assessment. Results: A total of 572 proteins were identified. Although no proteins fulfilled strict exclusivity criteria for a single cause-of-death group, differential expression analysis revealed distinct molecular patterns distinguishing ischemic, congestive, and non-cardiovascular deaths. Thirty-one proteins were differentially expressed between ischemic and congestive cases, including α-1 antitrypsin (AAT), plasma levels did not demonstrate statistically significant discrimination. In contrast, plasma Apolipoprotein A-IV (ApoA-IV) levels were significantly associated with ischemic death in regression models, and ROC analysis yielded a cutoff point with complete separation between ischemic and selected non-cardiovascular cases. However, the limited sample size warrants cautious interpretation due to potential overfitting. Conclusions: Postmortem cardiac proteomic profiling reveals biologically coherent molecular signatures associated with different cardiovascular causes of death. Although further validation in larger independent cohorts is required, ApoA-IV emerges as a promising candidate biomarker for ischemic cardiac death. Multimarker proteomic strategies may complement traditional autopsy to enhance diagnostic accuracy in forensic investigations, particularly in cases with equivocal morphological findings. Full article

The growing global population and increasing pressure on conventional food systems have intensified the search for sustainable and nutrient-rich protein sources. Blue foods derived from marine and freshwater organisms offer significant nutritional advantages and lower environmental footprints compared with many terrestrial animal proteins. However, challenges related to resource sustainability, processing, preservation, and product traceability limit their full potential. This review provides a broad overview of emerging technologies shaping the future of blue food systems, covering innovative production strategies, advanced processing techniques, and omics-based analytical approaches. Key developments in cellular aquaculture and cellular mariculture are discussed as promising alternatives to traditional fisheries and aquaculture, enabling the production of blue food through controlled cell cultivation. Additionally, alternative protein platforms including plant-based, fermentation-derived, and cultivated blue food analogues are assessed for their potential to enhance sustainability and diversify aquatic protein sources. Advanced structuring technologies such as extrusion, electrospinning, wet spinning, and 3D printing are highlighted for their roles in developing blue food analogues with improved texture and sensory attributes. Furthermore, non-thermal preservation techniques, including cold plasma (CP), high-pressure processing (HPP), pulsed electric fields (PEFs), and ultraviolet-based treatments, are reviewed for their effectiveness in improving microbial safety and extending shelf life while maintaining nutritional quality. The integration of omics technologies (proteomics, metabolomics, and lipidomics) provides deeper molecular insights into product quality, authenticity, and traceability within blue food supply chains. Collectively, these interdisciplinary advancements demonstrate strong potential to transform blue food production into a more resilient, sustainable, and technology-driven sector. Future progress will depend on overcoming challenges related to scalability, regulatory frameworks, and consumer acceptance to enable the successful commercialization of next-generation blue food products. Full article

Extracellular vesicles (EVs) mediate intercellular communication by delivering proteins and RNAs, with their molecular cargo often reflecting the biological context of their source. Perinatal tissues are promising sources of EV-related biomaterials with potential dermatologic applications. In this study, we compared EV-related molecular cargo from two umbilical cord-associated sources, umbilical cord mesenchymal stem cell (UCMSC)-derived EVs and cord blood plasma (CBP), to investigate whether these materials exhibit distinct functional effects on melanogenesis. UCMSC-derived EVs were isolated from conditioned culture medium and characterized using nanoparticle tracking analysis (NTA), cryo-electron microscopy (cryo-EM), and canonical EV marker detection, while cord blood samples were processed to obtain plasma following centrifugation and filtration, containing EVs together with soluble plasma components. Functional assays in the murine melanocyte cell line B16F10 demonstrated that UCMSC-derived EVs suppressed melanin production, whereas CBP treatment enhanced melanogenesis. Integrative omics analyses combining microRNAs (miRNAs) microarray profiling and proteomic characterization revealed distinct molecular signatures between UCMSC-derived EVs and CBP samples. Functional validation using miRNA mimic assays showed that selected miRNAs, including miR-6862-5p, miR-3622b-5p, miR-7847-3p, miR-6774-5p, and miR-4685-5p, reduced melanin production, whereas others, including miR-203a-3p, miR-126-3p, miR-139-5p, and miR-15b-5p, increased melanin levels. Pathway analysis using Ingenuity Pathway Analysis (IPA) (QIAGEN Inc.) associated these miRNA subsets with signaling pathways involved in melanogenesis. Together, these findings indicate that UCMSC-derived EVs and CBP exhibit opposite functional effects on melanogenesis and possess distinct miRNA and protein cargo profiles, providing potential molecular targets for modulating pigmentation and supporting the development of EV-related therapeutic strategies for pigmentation disorders. Full article

Gamma-tocotrienol (GT3) is one of the constituents of vitamin E that demonstrated significant radioprotective efficacy in murine and nonhuman primate (NHP) models. Considering the antioxidant activity of GT3 and its role in terminating lipid peroxidation, we hypothesize that mechanism of radioprotective effect of GT3 may involve the inhibition of irradiation-induced ferroptosis—a form of regulated cell death characterized by excessive, iron-dependent, peroxidation of lipids in cellular membranes. To test this hypothesis, the metabolomic and proteomic data from serum samples of GT3- or vehicle-treated NHPs exposed to 12 Gy (partial- or total-body) radiation was analyzed with focus on lipid peroxidation markers and proteins involved in iron metabolism. Four secondary lipid peroxidation products were identified including 4-oxo-2-nonenal (4-ONE), 4-hydroperoxy-2-nonenal (4-HPNE), 3,4-epoxynonanal (3,4-ENA), and trans-4,5-epoxy-(2E)-decenal (4,5-EDE). In vehicle-treated animals, their concentrations increased significantly as soon as 4 h after irradiation and then gradually declined. GT3 treatment mitigated this radiation-induced increase. In addition to lipid peroxidation products, similar patterns of change were observed for several polyunsaturated, monounsaturated, and saturated fatty acids as well as amino acids such as lysine and its derivatives. Taken together, these metabolomic changes suggest that irradiation induces cellular membrane damage through enhanced lipid peroxidation, while GT3 exerts a protective effect against this process. In addition, GT3 increased serum levels of haptoglobin and hemopexin—two plasma scavenger proteins that play complementary protective roles in iron and heme homeostasis. Although the present study does not conclusively demonstrate that GT3 mediates radioprotection via inhibition of ferroptosis, the data suggest that GT3 limits membrane damage and reduces susceptibility to ferroptosis by enhancing iron and heme scavenging. Further investigation into the interaction between GT3 and key components of ferroptosis following exposure to ionizing radiation is therefore warranted. Full article

Cystathionine β-synthase (CBS) deficiency causes classical homocystinuria with severe hyperhomocysteinemia (HHcy) that is inadequately controlled by current therapies. We tested whether liver-targeted CBS gene therapy provides durable biochemical and phenotypic rescue. Using a Cre-inducible adult mouse model of whole-body CBS loss, a single intravenous dose of AAV-DJ-hCBS (3 × 10¹² or 3 × 10¹³ vg/kg) was administered, and the animals were followed for 12 months. Vector biodistribution showed ~100-fold hepatic enrichment over the kidney and spleen. Both doses rapidly normalized plasma homocysteine (<8 µM), maintaining correction throughout the study while preventing alopecia, weight loss, and loss of adiposity. Liver histology showed resolution of inflammation, and only 2 of 19 mice developed anti-hCBS antibodies. Liver proteomics (3998 proteins quantified) revealed CBS deficiency-associated suppression of tRNA aminoacylation and dysregulation of lipid and carbon metabolism with an HNF4A transcriptional signature, all normalized by therapy. Liver metabolomics demonstrated accumulation of S-adenosylmethionine and S-adenosylhomocysteine and disruption of phosphatidylcholine synthesis, also corrected by treatment. Plasma metabolomics revealed systemic disturbances fully normalized by hepatic CBS restoration. These findings identify the liver as the central metabolic control point in CBS deficiency and support liver-targeted gene therapy as a durable corrective strategy. Full article

Background: Neurodegenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD) are increasingly recognized as biologically heterogeneous disorders. Although biomarker-based frameworks have improved disease stratification, they may not fully capture the molecular diversity underlying disease mechanisms. This study aimed to define biologically meaningful AD and PD subtypes by employing large-scale plasma proteomics to characterize mechanism-driven patient stratification. Methods: We analyzed plasma proteomic data from the Global Neurological Proteomics Consortium (GNPC) dataset and performed disease-specific unsupervised clustering to identify molecular subtypes. We performed differential protein expression and pathway enrichment analyses to characterize subtype-specific and shared biological signatures. Results: Clustering analysis revealed three molecular AD subtypes and two PD subtypes, each exhibiting unique proteomic signatures despite similar demographic and cognitive profiles. AD subtypes differed in the relative involvement of immune activation, mitochondrial dysfunction, synaptic signaling, and calcium-related pathways, whereas PD subtypes showed divergence in neuroinflammatory, oxidative stress, and mitochondrial programs. Conclusions: We demonstrated stratification of AD and PD into molecular subtypes, potentially supporting scalable, mechanism-directed stratification and the development of future targeted, disease-modifying therapies. Full article

Background/Objectives: Multiple myeloma (MM) is an incurable plasma cell neoplasm in which diagnosis and prognostication rely on invasive bone marrow examinations that may not capture biological heterogeneity across different disease sites. There is a clinical need for non-invasive biomarkers that can accurately predict treatment outcomes. Methods: We performed a global proteomic profiling of bone marrow-derived extracellular vesicles (EVs) from nine MM patients and ten controls. A total of 8839 proteins were identified, of which 14 met predefined selection criteria. These candidates were quantified in serum-derived EVs using targeted proteomic analysis. Prognostic relevance of selected proteins was evaluated in newly diagnosed MM (NDMM) patients treated with daratumumab-containing frontline regimens (n = 26) and healthy individuals (n = 60). Progression-free survival (PFS) was analyzed using univariable and multivariable models. Results: IL5RA (p = 0.003) and BCMA (p < 0.001) were significantly elevated in serum EVs from MM patients compared with controls. Higher serum EV-IL5RA and EV-BCMA were associated with a trend toward shorter PFS. Combined assessment of these biomarkers enabled clear stratification of MM patients into three prognostic groups, including a cohort with markedly inferior outcomes, with a 20-month PFS of 0 (p = 0.001). In multivariable analysis, the combined serum EV-IL5RA and EV-BCMA signature suggests an independent prognostic potential (HR = 38.49 [95% CI, 1.51–47.79], p = 0.015). Conclusions: Serum EV-IL5RA and EV-BCMA are novel non-invasive biomarkers, measurable through routine blood testing, with strong potential to improve risk stratification in NDMM patients in the era of daratumumab-based frontline therapy. Full article

Background: Lipoprotein(a) [Lp(a)] is a genetically determined risk factor for atherosclerotic cardiovascular disease (ASCVD). Proteomic studies suggest that Lp(a)-associated proteins mediate inflammation, thrombosis, and vascular calcification, but methodological variability may influence proteome definition. Methods: Lp(a) was immunoprecipitated from human plasma using an apo(a)-specific monoclonal antibody and analyzed by mass spectrometry following either in-gel digestion or automated in-solution proteolysis. Proteins identified by ≥3 unique peptides and consistently detected across all samples by both methods were considered high confidence. Functional enrichment and interaction networks were assessed using STRING. Results: In-solution proteolysis identified 92 proteins and in-gel digestion identified 55 proteins, with 34 proteins shared between methods. These high-confidence proteins were enriched for pathways involved in lipoprotein remodeling, coagulation regulation, vesicle-mediated transport, lipid binding, and extracellular matrix organization, providing biological insight into mechanisms linking Lp(a) to inflammation, thrombosis, and calcification. Conclusions: Proteome composition of Lp(a) is method-dependent; however, a rigorously defined core proteome of 34 proteins was consistently identified across analytical approaches, highlighting biologically relevant pathways that may underlie Lp(a)-mediated ASCVD risk. Full article