Search Results (10,279)

Interferon Regulatory Factor 5 plays an important role in the regulation of innate immune responses by amplifying the Nuclear Factor κB response, which is critical in gout inflammation. Furthermore, the rs4728141 polymorphism C allele was associated with both increased IRF5 expression and susceptibility to gout. We examine the association between rs4728141 and cytokine production in response to various Toll-Like Receptor ligands and describe the transcriptomic and proteomic changes observed in patients with gout and controls in relation to this polymorphism. We examine the transcriptome of freshly isolated peripheral blood mononuclear cells (PBMCs) from 93 normouricemic donors and 63 gout patients as well as serum inflammatory proteome in 197 control and 195 gout samples. Stimulation experiments of freshly isolated human PBMCs were performed over 24 h, followed by RNA-sequencing in gout patients and cytokine production measurement by ELISA in normouricemic donors and gout patients. The rs4728141 C allele was associated with increased IL-1β expression in unstimulated PBMCs of controls, but not in gout. No association between the polymorphism and serum inflammatory proteome was found. As expected, an increased IRF5 expression was observed in stimulated PBMCs of rs4728141 C allele carriers in response to several stimulations. Interestingly, IL-1β production was specifically enhanced in association to the rs4728141 C allele when cells were stimulated with palmitate with or without monosodium urate crystals. This pattern of cytokine production shows a functional impact of rs4728141 in gout through altered IL-1β production. Full article

Glycosylation of surface proteins is a crucial post-translational modification that reflects the activation status of neutrophils, the predominant leukocyte subset in humans and horses. Neutrophils have emerged as active contributors to diseases mediated by the adaptive immune system, such as equine recurrent uveitis (ERU), a sight-threatening disease in horses and a unique model for studying the pathogenesis of autoimmune uveitis in humans. Since changes in surface glycosylation can impact neutrophil function, we were interested in the surface glycosylation landscape on neutrophils from healthy horses and the potential changes in surface glyco-signatures in ERU. Using 35 different plant lectins, we outlined a profile of surface-exposed glycan moieties on equine neutrophils and detected significantly increased O-glycosylation in a diseased state through Jacalin (JAC) binding via flow cytometry. Subsequent molecular weight comparison of JAC pull-down assay data and neutrophil proteomics indicated the surface proteins Integrin beta-2 and CUB domain-containing protein 1 as potential anchors for increased O-glycan levels in ERU. These findings give novel insights into neutrophil surface glycosylation in health and disease and propose O-glycosylation as a possible biomarker for autoimmune uveitis. Full article

Focal cortical dysplasia (FCD) is a major cause of drug-resistant epilepsy, yet its molecular basis remains poorly understood. Numerous studies have analyzed RNA, protein, and microRNA alterations, but results are often inconsistent across subtypes and methodologies. To address this gap, we conducted a systematic review integrating transcriptomic, proteomic, and microRNA data from 117 human studies of FCD subtypes I–III. Differentially expressed factors were extracted, categorized by subtype, and analyzed using pathway enrichment and network approaches. Our integrative analysis revealed convergent dysregulation of neuroinflammatory, synaptic, cytoskeletal, and metabolic pathways across FCD subtypes. Consistently altered genes, including IL1B, TLR4, BDNF, HMGCR, and ROCK2, together with dysregulated microRNAs such as hsa-miR-21-5p, hsa-miR-155-5p, and hsa-miR-132-3p, were linked to PI3K–Akt–mTOR, Toll-like receptor, and GABAergic signaling, emphasizing shared pathogenic mechanisms. Importantly, we identified overlapping transcript–protein patterns and subtype-specific molecular profiles that may refine diagnosis and inform therapeutic strategies. This review provides the first cross-omics molecular framework of FCD, demonstrating how convergent pathways unify heterogeneous findings and offering a roadmap for biomarker discovery and targeted interventions. Full article

Scorpion venom is a rich source of bioactive compounds with significant potential for anticancer drug development. Its diverse molecular composition, including neurotoxins, antimicrobial peptides, and enzymes, provides a vast library for therapeutic innovation. Proteomic analyses have characterized venom composition in several species, while further functional assays have clarified their anticancer mechanisms. This review synthesizes current knowledge on scorpion venom-derived peptides with demonstrated anticancer activity, which selectively target ion channels, induce apoptosis, or disrupt tumor microenvironments. Where available, we highlight proteomic studies that have identified these components and discuss their structural features relevant to drug design. We also examine clinical applications and the challenges in translating venom peptides into therapies. The crucial and growing role of proteomics in this field, particularly for venom fractionation, component identification, and structural characterization, is critically evaluated. Full article

The plasma membrane (PM) of eukaryotic cells plays a key role in the response to stress, acting as the first line of defense against environmental changes and protecting cells against intracellular perturbations. In this work, we explore how membrane-bound chaperones and membrane lipid domains work together to shape plasma membrane properties—a partnership we refer to as the “epichaperome–plasma membrane lipid axis.” This axis influences membrane fluidity, curvature, and domain organization, which in turn shapes the spatial and temporal modulation of signaling platforms and pathways essential for maintaining cellular integrity and homeostasis. Changes in PM fluidity can modulate the activity of ion channels, such as transient receptor potential (TRP) channels. These changes also affect processes such as endocytosis and mechanical signal transduction. The PM proteome undergoes rapid changes in response to membrane perturbations. Among these changes, the expression of heat shock proteins (HSPs) and their accumulation at the PM are essential mediators in regulating the physical state and functional properties of the membrane. Because of the pivotal role in stress adaptation, HSPs influence a wide range of cellular processes, which we grouped into three main categories: (i) mechanistic insights, differentiating in vitro (liposome, reconstituted membrane systems) and in vivo evidence for HSP-PM recruitment; (ii) functional outputs, spanning how ion channels are affected, changes in membrane fluidity, transcytosis, and the process of endocytosis and exosome release; and (iii) pathological effects, focusing on how rewired lipid–chaperone crosstalk in cancer drives resistance to drugs through altered membrane composition and signaling. Finally, we highlight Membrane Lipid Therapy (MLT) strategies, such as nanocarriers targeting specific PM compartments or small molecules that inhibit HSP recruitment, as promising approaches to modulate the functional stability of epichaperome assembly and membrane functionality, with profound implications for tumorigenesis. Full article

Leaf senescence is a developmental process that allows nutrients to be remobilized and transported to sink organs. Previously, papain-like cysteine proteases (PLCPs) have been found to be highly expressed during leaf senescence in different plant species. In this study, we analyzed active PLCPs in barley (Hordeum vulgare L.) leaves during the terminal stage of natural senescence. Anion exchange chromatography of protein extracts from barley leaves, harvested six weeks after anthesis, followed by activity assays using the substrates Z-FR-AMC and Z-RR-AMC, revealed a single prominent peak corresponding to active PLCPs. This hydrolytic activity was completely inhibited by E-64, a potent and irreversible inhibitor of cysteine proteases. Fractions enriched for PLCP activity were affinity-labeled with DCG-04 and subjected to SDS-PAGE fractionation, separating two major bands at 43 and 38 kDa. These bands were analyzed using tandem mass spectrometry, allowing the identification of eleven PLCPs. Identified enzymes belong to eight PLCP subfamilies, including CTB/cathepsin B-like (HvPap-19 and -20), RD19/cathepsin F-like (HvPap-1), ALP/cathepsin H-like (HvPap-12 or aleurain), SAG12/cathepsin L-like A (HvPap-17), CEP/cathepsin L-like B (HvPap-14), RD21/cathepsin L-like D (HvPap-6 and -7), cathepsin L-like E (HvPap-13 and -16), and XBCP3 (HvPap-8). Among the identified PLCPs, HvPap-6 was the most abundant. Peptides corresponding to HvPap-6 were identified in both the 43 kDa and 38 kDa bands in approximately the same quantity based on total spectral count. Thus, our results indicate that two active HvPap-6 isoforms can be isolated from barley leaves at late senescence. Full article

Background: EHEC O157:H7 causes severe gastrointestinal illness by first colonizing the large intestine. It intimately attaches to the epithelial lining, orchestrating distinctive “attaching and effacing” lesions that disrupt the host’s cellular landscape. While much is known about the well-established virulence factors, there are much to learn about the surface proteins’ roles in a living host. Methods: This study presents the first in vivo characterisation of the surface proteome, i.e., proteosurfaceome, of Escherichia coli O157:H7 EDL933 during intestinal infection, revealing spatial and temporal adaptations critical for colonisation and survival. Using a murine ileal loop model, surface proteomic profiles were analysed at early (3 h) and late (10 h) infection stages across the ileum and colon. Results: In total, 272 proteins were identified, with only 13 shared across all conditions, reflecting substantial niche-specific adaptations. Gene ontology enrichment analyses highlighted dominant roles in metabolic, cellular, and binding functions, while subcellular localisation prediction uncovered cytoplasmic moonlighting proteins with surface activity. Comparative analyses revealed dynamic changes in protein abundance. Conclusions: These findings indicate a coordinated shift from stress adaptation and virulence to nutrient acquisition and persistence and provide a comprehensive view of EHEC O157:H7 surface proteome dynamics during infection, highlighting key adaptive proteins that may serve as targets for future therapeutic and vaccine strategies. Full article

Maize (Zea mays L.), as a globally significant cereal crop, exhibits high sensitivity to salt stress during early seedling stages. Although melatonin (MT) has demonstrated potential in mitigating abiotic stresses, the specific mechanisms underlying MT-mediated alleviation of salt stress in maize seedlings remain unclear. In this study, we established four treatment groups: control (CK), melatonin treatment (MT), salt stress (NaCl), and combined treatment (NaCl_MT). Metabolomic and proteomic analyses were performed, supplemented by photosynthesis-related experiments as well as antioxidant-related experiments. Metabolomic analysis identified key metabolites in MT-mediated salt stress mitigation. Both metabolomic and proteomic analyses underscored the critical roles of photosynthetic and antioxidant pathways. Salt stress significantly decreased the net photosynthetic rate (Pn) by 67.7%, disrupted chloroplast ultrastructure, and reduced chlorophyll content by 41.6%. Conversely, MT treatment notably mitigated these detrimental effects. Moreover, MT enhanced the activities of antioxidant enzymes by approximately 10–20% and reduced the accumulation of oxidative stress markers by around 10–25% in maize seedlings under salt stress. In conclusion, this study conducted a systematic and multidimensional investigation into the mitigation of salt stress in maize seedlings by MT. Our results revealed that MT enhances antioxidant systems, increases chlorophyll content, and alleviates damage to chloroplast ultrastructure, thereby improving photosystem II performance and strengthening photosynthesis. This ultimately manifests as improved seedling phenotypes under salt stress. These findings provide a meaningful entry point for breeding salt-tolerant maize varieties and mitigating the adverse effects of salinized soil on maize growth and yield. Full article

Biological control with beneficial bacteria offers a sustainable alternative to synthetic agrochemicals for managing plant pathogens and enhancing plant health. However, bacterial biocontrol agents (BCAs) remain underexploited due to regulatory hurdles (such as complex registration timelines and extensive dossier requirements) and limited strain characterization. Recent advances in omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have strengthened the bioprospecting pipeline by uncovering key microbial traits involved in biocontrol. Genomics enables the identification of biosynthetic gene clusters, antimicrobial pathways, and accurate taxonomy, while comparative genomics reveals genes relevant to plant–microbe interactions. Metagenomics uncovers unculturable microbes and their functional roles, especially in the rhizosphere and extreme environments. Transcriptomics (e.g., RNA-Seq) sheds light on gene regulation during plant-pathogen-bacteria interactions, revealing stress-related and biocontrol pathways. Metabolomics, using tools like Liquid Chromatography–Mass Spectrometry (LC-MS) and Nuclear Magnetic Resonance spectroscopy (NMR), identifies bioactive compounds such as lipopeptides, Volatile Organic Compounds (VOCs), and polyketides. Co-culture experiments and synthetic microbial communities (SynComs) have shown enhanced biocontrol through metabolic synergy. This review highlights how integrating omics tools accelerates the discovery and functional validation of new BCAs. Such strategies support the development of effective microbial products, promoting sustainable agriculture by improving crop resilience, reducing chemical inputs, and enhancing soil health. Looking ahead, the successful application of omics-driven bioprospection of BCAs will require addressing challenges of large-scale production, regulatory harmonization, and their integration into real-world agricultural systems to ensure reliable, sustainable solutions. Full article

Transmembrane proteins (TMPs) constitute approximately 30% of the mammalian proteome and are critical targets in biomedical research due to their involvement in signaling, transport, and drug interactions. However, their unique structural characteristics pose significant challenges for conventional multiple sequence alignment (MSA) methods, which are typically optimized for soluble proteins. In this paper, we propose TMP-M2Align, a novel topology-aware multiobjective algorithm specifically designed for the multiple alignment of TMPs. The method simultaneously optimizes two complementary objectives: (i) a topology-aware Sum-of-Pairs (SPs) score that integrates region-specific substitution matrices and gap penalties, and (ii) an Aligned Regions (ARs) score that rewards consistent alignment of functional and topological domains. By combining these objectives, TMP-M2Align generates Pareto front approximations of alignment solutions, enabling researchers to select trade-offs that best suit their biological questions. We evaluated TMP-M2Align on BAliBASE Reference Set 7 and on complete datasets of human G protein-coupled receptors (GPCRs) from classes A, B1, and C. Experimental results demonstrate that TMP-M2Align consistently outperforms both traditional alignment tools and specialized TM-specific methods in terms of SPs and Total Column metrics. Moreover, qualitative topological analyses confirm that TMP-M2Align preserves the integrity of transmembrane helices and loop boundaries more effectively than competing approaches. These findings highlight the effectiveness of integrating topology-aware scoring with multiobjective optimization for achieving accurate and biologically meaningful alignments of TMPs. Full article

The study presents the potential of milkfish frame, a by-product of milkfish processing, as a source of dipeptidyl peptidase IV (DPP-IV) inhibitory and antioxidant peptides with potential applications in type 2 diabetes management. Proteomic analysis identified key proteins, including 65 kDa warm temperature acclimation protein 1 and myosin heavy chain. In silico prediction (BIOPEP-UWM) guided the selection of proteases for generating DPP-IV inhibitory peptides. Enzymatic hydrolysates were produced and evaluated for bioactivity. Among the treatments, pepsin hydrolysis (2% v/v, 8 h) yielded the highest peptide content (283.64 mg/g), soluble protein (86.46%), and DPP-IV inhibitory activity (68.47%). The resulting milkfish frame pepsin hydrolysate (MFH) was further enhanced through ultrafiltration and simulated gastrointestinal digestion, which improved the DPP-IV inhibitory and antioxidant capacities. Cytotoxicity assays confirmed that MFH (0–100 μg/mL) was non-toxic to FL83B hepatocytes after 24 h. Moreover, treating TNF-α-induced FL83B cells with 10 μg/mL MFHs improved cell viability, reducing the toxicity induced by TNF-α in cells. These findings show that MFHs exhibit promising antidiabetic potential and could serve as natural alternatives to synthetic drugs for type 2 diabetes management. This also demonstrates the valorization of fish processing by-products into functional food ingredients, advancing sustainable approaches in food innovation. Full article

Current standard treatments for osteosarcoma have not been changed for decades and have limited and variable success. The advancement of precision medicine technologies, along with the drug-repurposing and fast drug-screening methodologies available, has opened new avenues for the development of more effective therapeutic strategies. In this study, we evaluated the effectiveness of halogenated boroxine (HB) and dextran-coated cerium oxide nanoparticles—DexCeNPs (SD2)—in an in vitro osteosarcoma model. Both agents were tested individually and in combination. The research encompassed assessments of treatment-related cytotoxicity and cell viability, oxidative stress, and apoptotic and necrotic responses, as well as the effects on 3D spheroid models. The results demonstrated that the effects of HB and SD2 were strongly influenced by the dose, exposure time, and cell type. Both exhibited distinguished antitumor activity through cytotoxicity and specific reactive oxygen species (ROS) induction. The combined treatment produced modulated responses that were dependent on the treatment ratio and cell line, suggesting potential synergistic or selective interactions. Notably, the outcomes of the analysis conducted in 3D models revealed reduced toxicity toward non-tumor cells. These findings suggest the improved efficacy of HB and SD2 used in combination as a selective and novel antitumor strategy and underscore the need for further mechanistic studies at the transcriptomic and proteomic levels to elucidate the underlying pathways and clarify the mechanisms of action. Full article

Galectins, a family of glycan-binding proteins, play crucial roles in various cellular functions, acting at both intracellular and extracellular levels. Among them, Galectin-3 (Gal-3) stands out as a unique member, possessing an intrinsically unstructured N-terminal oligomerization domain and a canonical carbohydrate-recognition domain (CRD). Gal-3 binding to glycosylated plasma membrane cargo leads to its oligomerization and membrane bending, ultimately resulting in the formation of endocytic invaginations. An interactomic assay using proteomic analysis of endogenous Gal-3 immunoprecipitates identified the orphan G protein-coupled receptor GPRC5A as a novel binding partner of Gal-3. GPRC5A, also known as Retinoic Acid-Induced protein 3 (RAI3), is transcriptionally induced by retinoic acid. Our results further demonstrate that extracellular recombinant Gal-3 stimulates GPRC5A internalization. In SW480 colorectal cancer cells, glycosylated GPRC5A interacts with Gal-3. Interestingly, while GPRC5A expression was upregulated by the addition of all-trans retinoic acid (ATRA), its endogenous internalization in SW480 cells was specifically triggered by extracellular Gal-3, but not by ATRA. This study provides new insights into the endocytic mechanisms of GPRC5A, for which no specific ligand has been identified to date. Further research may uncover additional Gal-3-mediated functions in GPRC5A cellular signaling and contribute to the development of innovative therapeutic strategies. Full article

Schizophrenia is a highly polygenic and clinically heterogeneous disorder. We first review layer-specific evidence across genetics, epigenetics, transcriptomics, proteomics, and patient-derived induced pluripotent stem cell (iPSC) models, then integrate cross-layer findings. Genetics research identifies widespread risk architecture. Hundreds of loci from common, rare, and CNV analyses. Epigenetics reveals disease-associated DNA methylation and histone-mark changes. These occur at neuronally active enhancers and promoters, together with chromatin contacts that link non-coding risk to target genes. Transcriptomics show broad differential expression, isoform-level dysregulation, and disrupted co-expression modules. These alterations span synaptic signaling, mitochondrial bioenergetics, and immune programs. Proteomics demonstrates coordinated decreases in postsynaptic scaffold and mitochondrial respiratory-chain proteins in cortex, with complementary inflammatory signatures in serum/plasma. iPSC models recapitulate disease-relevant phenotypes: including fewer synaptic puncta and excitatory postsynaptic currents, electrophysiological immaturity, oxidative stress, and progenitor vulnerability. These same models show partial rescue under targeted perturbations. Integration across layers highlights convergent pathways repeatedly supported by ≥3 independent data types: synaptic signaling, immune/complement regulation, mitochondrial/energetic function, neurodevelopmental programs and cell-adhesion complexes. Within these axes, several cross-layer convergence genes/proteins (e.g., DLG4/PSD-95, C4A, RELN, NRXN1/NLGN1, OXPHOS subunits, POU3F2/BRN2, PTN) recur across cohorts and modalities. Framing results through cross-layer and shared-pathway convergence organizes heterogeneous evidence and prioritizes targets for mechanistic dissection, biomarker development, and translational follow-up. Full article

Background: Extracellular vesicles, particularly exosomes, play a crucial role in cell–cell communication and as carriers of biomarkers. However, their use in clinical settings is limited due to a lack of standardized isolation and characterization. Ultracentrifugation (UC) is considered a gold standard for exosome isolation but presents several limitations. Size-exclusion chromatography (SEC) has recently gained attention as a superior method, which offers better yield, purity, and protection of exosome physical properties. This study focused on optimizing the SEC method for isolation of exosomes from seminal plasma and comparing yield, quality, and proteome profiles with those obtained by UC. Methods: In this SEC method, seminal plasma (0.5 mL) was loaded onto a SEC column and collected in 13 fractions of 0.4 mL each. The physical and molecular characterization of exosomes was carried out using a ZetaView analyzer and Western blot, respectively. Further, SEC-isolated exosomes were used for proteomic profiling and functional bioinformatic analysis. Results: The second and third fractions had the highest concentration of exosomes with uniform size and strong expression of exosome markers. Also, comparative proteomic analysis identified 3315 proteins in SEC-isolated exosomes and 931 in UC-isolated exosomes, with 709 proteins in common. SEC-isolated exosomes showed greater overlap with Vesiclepedia’s and ExoCarta’s top 100 lists than UC-isolated exosomes (Vesiclepedia: 91 vs. 77 proteins, ExoCarta: 94 vs. 79). Proteins from SEC- and UC-isolated exosomes showed similar enrichment profiles across all three gene ontology categories. Conclusions: Overall, this optimized SEC protocol is a reliable alternative method to isolate seminal exosomes with high purity, supporting its potential applications in clinical and basic research. Full article