Search Results (5,689)

Pediatric brain tumor survivors remain at high risk of recurrence, yet current surveillance strategies relying on neuroimaging and cerebrospinal fluid (CSF) cytology have limited sensitivity for early or minimal disease. Tumor-specific peptides (TSPs) derived from individual tumors represent a promising class of highly specific biomarkers for longitudinal disease monitoring through CSF-based proteomic analysis. In this study, tumor tissue and serial CSF samples from six pediatric brain tumor patients (five medulloblastomas and one atypical teratoid/rhabdoid tumor (ATRT)) were analyzed using an integrated proteogenomic workflow combining discovery and targeted mass spectrometry. TSPs were identified from resected tumor tissue and matched against shotgun CSF proteomic datasets to nominate candidate biomarkers. High-confidence peptides were synthesized as isotopically labeled standards and quantified longitudinally using targeted multiple reaction monitoring. Two TSP biomarkers derived from individualized pediatric brain tumors (one medulloblastoma and one ATRT) demonstrated robust detection in serial CSF samples and exhibited temporal concordance with radiographic disease course, declining with treatment response and increasing during disease progression. These findings establish the feasibility of detecting and longitudinally quantifying TSPs in CSF and support further investigation of individualized proteomic biomarkers for treatment response monitoring and disease surveillance in pediatric brain tumors. Full article

Background/Objectives: Human milk composition is shaped by gestational age at delivery and stage of lactation; however, proteomic differences between milk from mothers of preterm and term infants and their temporal patterns remain incompletely characterised. Methods: This prospective study enrolled 40 lactating mothers: 20 who delivered preterm infants (<32 weeks’ gestation) and 20 who delivered at term (37–42 weeks). Each provided milk samples during early lactation (first 10 days postpartum) and during later lactation (week five postpartum). Milk serum was analysed using quantitative data-independent acquisition mass spectrometry. Differential protein abundance was assessed separately at each time point; functional annotation was performed using Gene Ontology biological process analysis. Results: Eighty samples were analysed. On average, a total of 662 proteins were identified per sample, of which 169 were consistently quantified across all samples (1% FDR). During early lactation, 10 proteins differed significantly, with bidirectional changes and moderate effect sizes. At week five, 19 proteins were differentially abundant, predominantly higher in preterm samples. Immune-related proteins constituted the largest functional category at both stages. Immunoglobulin heavy constant gamma 4 remained consistently downregulated in preterm milk (1.6-fold lower abundance). Ferritin heavy chain (1.5) and HLA class II histocompatibility antigen gamma chain (1.8) were elevated only early, whereas calprotectin subunits S100A8 (5.6) and S100A9 (5.2) were markedly upregulated later. Conclusions: Proteomic differences vary across lactation stages, highlighting lactation stage as an essential contextual variable in comparative milk proteomics. Full article

Background/Objectives: Collagen hydrolysates are widely used as nutritional ingredients for skin and joint health; however, growing evidence indicates that collagen may also exert beneficial effects on cardiometabolic pathways. Short peptides have been shown to modulate angiotensin-converting enzyme (ACE) and dipeptidyl peptidase IV (DPP-IV), key regulators of blood pressure and glucose homeostasis. This study aimed to assess the dual ACE- and DPP-IV inhibitory and GLP-1 stimulation activities, respectively of a tripeptide-enriched formulation (CH). The study was performed using a benchmark collagen hydrolysate (BCH) as reference. Methods: ACE and DPP-IV inhibitory activities were evaluated using in vitro enzymatic assays. Cellular compatibility and in situ DPP-IV inhibition were assessed in Caco-2 intestinal cells, while glucagon-like peptide-1 (GLP-1) secretion was measured in STC-1 enteroendocrine cells. The degree of hydrolysis was determined by OPA assay, and nanoLC–HRMS was used to characterize and compare the proteomic profiles of the samples. Results: Both hydrolysates exhibited dose-dependent ACE and DPP-IV inhibition; however, CH showed significantly higher inhibitory activity at comparable concentrations. CH also reduced cellular DPP-IV activity in Caco-2 cells and stimulated GLP-1 secretion in STC-1 cells, whereas BCH showed limited or non-significant cellular effects. Peptidomic analysis revealed an enrichment of short- and medium-length peptides in CH, while BCH contained a higher proportion of long peptides (>2000 Da). Consistently, CH exhibited a 1.7-fold higher degree of hydrolysis than BCH. Conclusions: The tripeptide-enriched collagen hydrolysate demonstrated superior enzymatic and cellular bioactivity compared with the benchmark formulation, supporting its potential as a multifunctional bioactive ingredient for health applications. Full article

Chagas disease remains a major public health challenge and still lacks reliable serum biomarkers capable of accurately reflecting disease progression and therapeutic response. Here, we performed a quantitative label-free serum proteomic analysis in a murine model infected with two Trypanosoma cruzi strains exhibiting contrasting sensitivity to benznidazole (Be-78, sensitive; VL-10, resistant), evaluated during both acute and chronic phases, in the presence or absence of treatment. Distinct proteomic signatures were observed across strains, infection stages, and experimental groups, involving pathways related to complement activation, inflammatory responses, immunoglobulins, energy metabolism, and tissue remodeling. Markers of cellular injury, including LDH-A, C1q, and C6, remained predominantly elevated in mice infected with the benznidazole-resistant strain, whereas animals infected with Be-78 showed substantial proteomic normalization following treatment. In addition, structural proteins such as dystrophin, nebulin, alpha-adducin, and myosin XVIIIb clearly distinguished strain-dependent profiles of disease aggressiveness and tissue damage. Integrated analyses revealed that benznidazole efficacy is strongly influenced by the biological characteristics of the infecting strain and is directly mirrored in the serum proteome. Collectively, these findings identify promising serum biomarkers of tissue injury and therapeutic response and underscore the importance of parasite genetic variability in disease monitoring and in the development of improved diagnostic and therapeutic strategies. Full article

Background: Cholangiocarcinoma (CCA) is a highly heterogeneous malignancy in which numerous biomarker candidates have been reported, yet few progress to clinical use. Beyond biological complexity, this low translational yield reflects the lack of systematic criteria for prioritizing biomarkers during the discovery stage. In particular, tumor-derived signals identified in tissue often fail to persist in clinically accessible biofluids, as cross-compartment signal behavior is rarely evaluated explicitly. Methods: We developed an extracellular vesicle (EV)-guided, multi-compartment proof-of-concept framework to assess biomarker robustness and translatability early in discovery. EV proteomes from three biologically distinct CCA cell lines and a normal cholangiocyte were analyzed using multivariate and machine-learning-assisted approaches to identify conserved EV-associated features. These were integrated with public transcriptomic, epigenetic, copy-number, promoter usage, and miRNA regulatory data. Tissue relevance was assessed using TCGA/GTEx RNA-seq datasets, and exploratory signal behavior was examined in pooled serum- and urine-derived EVs from CCA patients and controls. Results: EV proteomics revealed marked molecular heterogeneity across CCA models but identified a small subset of conserved EV-associated proteins. SERPINF2 was used as a representative example, showing consistently reduced EV-associated abundance across all CCA models with coordinated regulation across multiple molecular layers. SERPINF2 expression was independent of patient sex and tumor stage and clearly distinguished tumor from normal bile duct tissue. Exploratory biofluid analyses demonstrated compartment-dependent signal behavior, with SERPINF2 depletion detectable in urine-derived EVs but not in serum-derived EVs. Conclusions: Rather than validating a single biomarker, this study presents an EV-guided, multi-compartment framework for prioritizing biomarker candidates at the discovery stage. By explicitly accounting for tumor heterogeneity and compartment-specific signal preservation, this proof-of-concept approach provides a practical decision-support strategy for identifying biomarkers with greater translational potential in heterogeneous cancers such as CCA. Full article

This study evaluated the effects of the dietary administration of a glycosylated form of active vitamin D (calcitriol, 1,25(OH)₂D₃) combined with ursolic acid (UA) and oleanolic acid (OA) triterpenes on sow health and productivity. Twenty-four third-parity Landrace × Large White sows were allocated at day 108 of gestation into three groups: a control group receiving 1800 IU/kg of vitamin D₃, and two treatment groups receiving the control diet supplemented with either 0.64 µg/kg (ACTD1) or 0.96 µg/kg (ACTD2) of glycosylated 1,25(OH)₂D₃ plus 140 or 210 µg/kg of UA + OA (4:1 ratio), respectively. Diets were administered from late gestation through the end of lactation. Farrowing duration, sow body weight, backfat thickness, and litter growth were recorded. Blood samples collected at key physiological stages were analyzed for pro-inflammatory cytokines, mineral homeostasis, endocrine markers, and serum proteome. Farrowing time was reduced in both treatment groups compared with the control (p < 0.05). Treated sows exhibited lower backfat thickness at the end of lactation and improved litter weights at farrowing, after cross-fostering, and at weaning (p < 0.05). Plasma pro-inflammatory cytokines (TNF-α, IL-1α, and IL-1β) were reduced at the end of lactation in ACTD1 and ACTD2 sows, with TNF-α and IL-1β already decreased after farrowing (p < 0.05). Treated sows also displayed decreased plasma parathormone concentrations at the end of lactation, along with increased circulating 1,25(OH)₂D₃ and calcium concentrations after farrowing and at lactation end (p < 0.05), while plasma phosphate levels remained unchanged. Proteomic analysis supported the systemic availability of the supplemented compounds and their involvement in metabolic and inflammatory pathways rather than calcium transport or vitamin D binding mechanisms. Overall, this nutritional strategy influenced the immune modulation while maintaining mineral homeostasis via modest endocrine adaptations. Larger-scale trials are warranted to confirm these results and to evaluate their practical applicability under commercial production conditions. Full article

Fruit ripening involves coordinated metabolic and molecular changes that shape quality traits, yet tissue-specific regulation in Selenicereus megalanthus remains unclear. Fruit development in S. megalanthus was investigated through an integrated analysis of pulp and peel across five developmental stages to elucidate tissue-specific metabolic and molecular regulatory dynamics. Proteomic profiling combined with targeted metabolomic analyses of sugars and phenolic compounds, multivariate statistics, and protein–protein interaction analysis was applied. A total of 411 proteins were identified in the pulp and 812 in the peel, of which 255 and 362 proteins, respectively, showed significant differential accumulation across development (p < 0.05), indicating higher regulatory plasticity in the peel. Multivariate analyses revealed clear stage-dependent reorganization of the proteome in both tissues. Functional annotation highlighted coordinated modulation of pathways related to cell wall remodeling, carbohydrate metabolism, antioxidant and detoxification systems, protein folding, and myo-inositol biosynthesis, directly associated with fruit texture and quality attributes. Metabolomic analyses revealed progressive sugar accumulation during ripening, with sucrose predominating at advanced stages, and pronounced tissue- and stage-dependent modulation of phenolic compounds, characterized by early enrichment in the pulp and sustained accumulation in the peel. Overall, these results demonstrate that yellow pitaya development involves tightly coordinated biochemical and regulatory mechanisms and identify the peel as a metabolically active tissue with relevance for postharvest management, fruit quality, and sustainable horticultural valorization. Full article

Huntington’s disease (HD) is characterized by progressive striatal atrophy and complex proteomic changes in the central nervous system. Using the ultrasensitive Next-Gen Ultra-Sensitive Immunoassay (NULISA) proteomic platform, we analyzed cerebrospinal fluid (CSF) from 88 persons with HD to dissect the biological correlates of gray matter loss. Our findings reveal a distinct “Two-Track” model of pathology. The first track, marked by the axonal damage protein neurofilament light chain (NEFL), showed a strong inverse correlation with putamen volume (Pearson r = −0.53, p < 0.001), reinforcing its utility as a proxy for structural neurodegeneration. The second track was defined by a positive association between the immune regulator TNFRSF8 (CD30) and putamen volume (Pearson r = 0.36, p < 0.001), reflecting a decline in active immune-regulatory signaling as striatal atrophy advances. Given its established role in immune modulation, TNFRSF8 was pre-specified for follow-up to further interrogate this neuro-immune axis. Crucially, TNFRSF8 maintained an independent association with striatal volume (Beta = 0.24, p = 0.008) even after controlling for NEFL, genetic burden (CAG-Age Product score), and sex. Supplementary analyses confirmed that this structural–immune axis is localized specifically to the striatum—showing no association with generic structural control regions—and is driven by CAG repeat length rather than chronological aging. Furthermore, bidirectional mediation analysis supported an atrophy-driven model, where striatal volume statistically mediates the relationship between genetic burden and downstream immune dysregulation (p = 0.010). These results demonstrate that maladaptive immune signaling is a distinct pathological correlate in HD, separable from general cytoskeletal damage. This dual-axis framework warrants evaluation in larger longitudinal and interventional studies to guide future biomarker-driven patient stratification and target engagement. Full article

Background: Individuals with type 2 diabetes mellitus (T2DM) are at markedly increased risk of developing coronary heart disease (CHD); however, the generalizability and transportability of existing prediction models remain uncertain. Objective: To identify and evaluate multivariable prognostic models developed to predict CHD in adults with T2DM. Methods: We conducted a PRISMA-guided systematic review and meta-analysis of multivariable prognostic models predicting CHD in T2DM populations. Model characteristics and performance metrics were extracted following the CHARMS and TRIPOD-SRMA frameworks, and pooled discrimination was estimated on the logit-transformed AUC scale using a random-effects model (REML, Hartung–Knapp adjustment). Between-study heterogeneity and 95% prediction intervals were quantified, while risk of bias and applicability were assessed using the PROBAST tool. Results: Thirteen studies encompassing clinical, imaging-based, and omics-augmented models met the inclusion criteria. The pooled AUC was 0.69 (95% CI: 0.66–0.71), with high heterogeneity (I² = 97.4%; τ² = 0.0979) and a wide 95% prediction interval (0.54–0.81). Classical regression-based models demonstrated modest discrimination, whereas machine learning, imaging, and proteomic approaches achieved higher AUC estimates but were frequently constrained by small sample sizes, internal-only validation, and poor calibration reporting. The analysis domain emerged as the principal source of bias in PROBAST evaluations, and applicability issues were most frequent in models requiring advanced imaging or molecular platforms. Conclusions: Prognostic models for CHD in T2DM demonstrate moderate-to-good discrimination but substantial heterogeneity and frequent miscalibration across studies. Their clinical utility depends on rigorous external validation and local recalibration, particularly when incorporating imaging or molecular predictors. Future research should prioritize standardized CHD outcomes, consistent calibration reporting, decision-analytic assessments, and the development of transportable multimodal prediction models across diverse populations. Full article

Avian influenza, a disease caused by avian influenza virus (AIV), mainly infects birds but can also infect mammals, which poses a serious threat to public health. Therefore, thorough understanding of its pathogenic mechanism and the identification of antiviral targets are essential for the prevention, control, and treatment of AIV. The polymerase acidic protein (PA) is a core component of the viral RNA-dependent RNA polymerase complex and plays a central role in viral transcription through its cap-snatching activity during early infection. We employed a multi-omics approach combining transcriptome analysis with PA interaction proteomics to characterize host responses during AIV infection and explore the PA–host interaction network. Transcriptomics revealed a polarized host response marked by activated translation-related processes, mitochondrial energy metabolism, and innate immune signaling, alongside broad suppression of nuclear transcriptional regulation and cell cycle pathways. Immunoprecipitation–mass spectrometry identified host proteins associated with PA that were enriched in RNA metabolism, ribosome biogenesis, and protein homeostasis. Integrative analysis of transcriptomic and interactome data, along with protein–protein interaction network analysis, prioritized a subset of high-confidence PA-interacting host factors. Among these, ribosomal protein RPS27A was validated to interact with PA and to support viral replication during early infection in this study. Full article

Background/Objectives: Molecular subtyping of pediatric B-cell acute lymphoblastic leukemia (B-ALL) has improved patient outcomes through stratification and selection of targeted therapies. Despite extensive genomic and transcriptomic profiling of this cancer, few studies to date have characterized the proteomic landscape, although proteins are the direct targets of many therapeutic agents. Methods: In this study, we demonstrate the utility of multi-omic integration of global transcriptomic, proteomic, and phosphoproteomic profiles of samples from patients diagnosed with either of two B-ALL subtypes—Ph-like (BCR::ABL1-like) and ETV6::RUNX1. Through individual and multi-omic analysis, we recapitulate known transcriptomic findings and identify novel subtype-specific proteomic and phosphoproteomic biomarkers. Conclusions: Our findings suggest a previously undescribed role for calcium-dependent signaling processes in Ph-like B-ALL, which has the potential to serve as a novel avenue for targeted treatments. By integrating multiple -omics modalities, we identify not only features of interest but also begin to unravel the regulatory interactions driving subtype-specific mechanisms of leukemogenesis. This integrated analytic approach paves the way for enhanced precision medicine for precise subtyping and treatment selection for pediatric leukemia patients. Full article

Biogenic carbon dots (CDs) are emerging as promising plant biostimulants, yet their effects during early crop establishment remain underexplored. Here, we synthesized and characterized Spirulina-derived CDs and evaluated their efficacy as seed nanopriming agents in rice (Oryza sativa L.). CDs exhibited nanoscale size, abundant surface functionalities, and a highly negative ζ-potential, indicative of stable aqueous dispersions. Spectroscopic characterization (Raman and FTIR) confirmed a graphitic–amorphous carbon structure. Near-infrared spectroscopy coupled to principal component analysis revealed time-dependent metabolic changes during imbibition, identifying 8–12 h as the optimal priming window. Nanopriming with Spirulina CDs (0.2 mg mL⁻¹ for 12 h) increased the seed germination rate (25%), the germination speed index (17%), vigor index I (22%), and root length (37%) compared to hydropriming. Biochemically, the nanoprimed seedlings accumulated higher levels of starch (24%), total carbohydrates (8%), and total phenolics (20%), without evidence of oxidative imbalance, based on antioxidant capacity measurements and proteomic profiling. Proteomic analysis revealed coordinated metabolic reprogramming, characterized by increased abundance of proteins involved in translation, energy metabolism, and ion/nutrient homeostasis, alongside reduced abundance of proteins associated with defense and catabolic processes. This shift from stress-preparation to growth-oriented metabolism supports improved seedling establishment. Overall, Spirulina-derived CDs function as effective nanobiostimulants that promote early metabolic activation and resource mobilization, offering a sustainable strategy to enhance rice seedling establishment. Full article

This study employed integrated transcriptomics and proteomics analysis to investigate the potential role of methionine (Met) in regulating the proliferation, differentiation, and lipid deposition of yak intramuscular preadipocytes (YIMA). Five Met concentrations (0, 0.05, 0.5, 5, and 50 mM) were used to establish the Met model of YIMA. The results of Bodipy, Oil Red O, EdU staining, and qPCR showed that the appropriate Met (0.05, 0.5, and 5 mM) supplementation significantly promoted the proliferation and adipogenic differentiation of YIMA, whereas excessive Met (50 mM) markedly inhibited these processes. To further evaluate the mechanism of Met on YIMA, cells supplemented with 0 mM (control, CON), 0.5 mM (moderate) and 50 mM (excessive) Met were selected for the transcriptomic and proteomic analyses. The results showed that moderate Met treatment primarily enriched pathways related to extracellular matrix–receptor interaction and the PI3K/AKT signaling pathway, while excessive Met significantly enriched processes involving abnormal methylation, DNA damage, and metabolic stress. Functional validation experiments further confirmed that Met regulates YIMA proliferation and differentiation by upregulating p-Akt protein expression and activating the PI3K/AKT pathway. These findings provide molecular insights that support improving yak meat quality and IMF content through dietary Met supplementation. Full article

Establishing plasma biomarkers in the veterinary field has always been a challenge, due to a lack of significant understanding of pathophysiological attributes of disease. Advances in mass spectrometry-based proteomic techniques have improved plasma biomarker discovery in veterinary medicine. Feline hypertrophic cardiomyopathy is the most common cardiac disease in cats and has a complex and not fully elucidated pathophysiology. This study aimed to use SWATH-MS proteomics to identify novel plasma biomarkers for fHCM and to further elucidate disease pathogenesis. Plasma was collected from 20 cats, consisting of healthy controls (n = 10) and a HCM group (n = 10). Cats with fHCM, were diagnosed by echocardiography and disease statuses were determined by a veterinary cardiologist. Undepleted cat plasma samples were digested using FASP and quantitative analysis was performed using DIA-NN. A total of 40 plasma proteins were found to be dysregulated, primarily associated with innate and humoral responses, including complement C7 and C9 and properdin proteins. Other dysregulated proteins were involved in blood coagulation (fibrinogen, fibulin-1), lipid metabolism (apolipoproteins), and inflammation pathways (transthyretin and plasminogen). These findings provide possible biomarkers for fHCM, with the potential to detect disease before clinical signs become evident, which is a significant outcome for fHCM. These proteomic changes suggest critical pathways for earlier intervention and could potentially lead to more effective treatment outcomes. Furthermore, having significant similarity to human disease strengthens the case for using cats as a potential translational model for hHCM. Full article

Background/Objectives: Hospital outbreaks of Pseudomonas aeruginosa are difficult to control due to the pathogen’s extensive repertoire, including its ability to form biofilms, adapt and persist in diverse environments, and develop multidrug resistance, all of which contribute to prolonged outbreaks. This study integrates the phenotypic, proteomic, and genomic characterization of a nosocomial outbreak comprising 38 clinical isolates and one environmental isolate recovered from the intensive care unit (ICU) of Hospital IESS Quito Sur. Methods: Clinical data were collected, antimicrobial susceptibility was assessed by minimum inhibitory concentration (MIC), carbapenemase genes were detected by multiple PCR and immunochromatographic assays, and the biofilm formation index (BFI) was determined. In addition, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used for species identification and clustering based on spectral similarity. Twelve representative isolates underwent whole genome sequencing (WGS) to characterize the resistome and virulome and to compare phylogenetic relationships with proteomic clustering defined by MALDI Biotyper Compass Explorer software. Results: All isolates were identified as P. aeruginosa, and phenotypic antimicrobial susceptibility classified most isolates as multidrug resistant, including 32 CRPA strains. The bla_VIM gene was detected in 22 isolates, while BFI analysis showed that all isolates formed moderate to strong biofilms. Genomic analysis revealed that most isolates belonged to ST111 and ST253, and both conserved and heterogeneous resistome and virulome profiles, with a broad distribution of determinants related to biofilm formation, stress tolerance, and persistence. Comparison between MALDI-TOF MS and WGS showed predominant concordance in clustering, mainly within subclusters but disagreement at the cluster level. Conclusions: The detection of carbapenemases, biofilm-forming ability, and virulence determinants associated with prolonged persistence highlights the need for integrated molecular tools, such as MALDI-TOF MS with MALDI Biotyper Compass Explorer software, to support epidemiological surveillance and to inform strategies aimed at mitigating prolonged hospital outbreaks caused by P. aeruginosa. Full article