Search Results (2,761)

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with a 5-year survival rate of 13.3%. First-line treatment relies on two chemotherapy regimens, FOLFIRINOX (FOLFNX) or gemcitabine plus nab-paclitaxel (GEMPAC). However, direct clinical comparisons between these regimens have yielded inconsistent results across survival and toxicity endpoints, and the molecular basis of heterogeneous treatment responses remains poorly defined. To investigate regimen-specific tumor-cell-intrinsic mechanisms, we performed quantitative proteomic profiling of a primary PDAC-derived MIA PaCa-2 cell line following treatment with FOLFNX or GEMPAC. Differentially expressed proteins were analyzed using Gene Ontology, KEGG, and Ingenuity Pathway Analysis to define pathway-level alterations, and findings were contextualized using TCGA transcriptomic data. Proteomic analyses revealed that FOLFNX and GEMPAC engage in distinct cytotoxic programs. FOLFNX predominantly suppressed ribosome biogenesis and mitochondrial translation, consistent with sustained metabolic and biosynthetic stress, whereas GEMPAC preferentially disrupted mitotic cytokinesis and phosphatidylinositol phosphate biosynthesis, consistent with mitotic failure. Integration with TCGA data showed that FOLFNX-altered proteins aligned with favorable prognostic expression signatures, whereas GEMPAC-associated proteins were enriched among adverse profiles, reflecting engagement of distinct tumor-intrinsic programs. Together, these findings provide mechanistic insight into differential chemotherapy responses and establish a foundation for proteomics-based biomarkers to guide personalized chemotherapy selection in PDAC. Full article

Vibrio alginolyticus is a foodborne pathogen commonly found in seafood and freshwater products, causing human illness through the consumption of tainted seafood. Small non-coding RNAs (sRNAs) take effect on the stability and translation of their target mRNAs by base-pairing, thereby quickly altering bacterial physiology and pathogenicity at the post-transcriptional level. This work constructed a label-free in-frame deletion mutant and a complement strain of micX, a cell-density-associated sRNA in V. alginolyticus. The ΔmicX mutant exhibited reduced growth and a reduction in the synthesis of exopolysaccharides, biofilm, and alkaline serine protease. A TMT-based quantitative proteomic analysis comparing ΔmicX with the wild-type strain identified 900 differentially expressed proteins, comprising 376 that were upregulated and 524 that were downregulated. The upregulated proteins are primarily associated with porin activity, transmembrane signaling receptor function, and the two-component system. The downregulated proteins are mainly engaged in processes including biofilm formation, cellular communication, and transmembrane transport activity. Of note, the expression levels of proteins involved in the type VI secretion system, exopolysaccharide synthesis, mannose-sensitive hemagglutinin type IV pili (MSHA), and biofilm formation were significantly reduced in the absence of micX. Furthermore, the expression levels of proteins associated with quorum sensing (particularly LuxR and AphA) changed significantly in the ΔmicX vs. WT comparison. These findings strengthened comprehension of the novel sRNA regulatory network and established a theoretical foundation for additional investigations into the virulence of V. alginolyticus. Full article

The interaction between Angiostrongylus vasorum and the vascular endothelium of the host plays a key role in the pathogenesis of canine angiostrongylosis. The adult stage of A. vasorum resides in right ventricles and pulmonary arteries of dogs and foxes and maintains close contact with the endothelium, whose activation may contribute to the hemostatic and hemorrhagic disorders observed in infected animals. However, the molecular mechanisms underlying this endothelial dysfunction remain poorly understood. To investigate this interaction, an in vitro model of vascular endothelial cells was stimulated with the adult A. vasorum homogenate. Quantitative proteomic analysis, combined with bioinformatic tools, identified 691 and 6011 protein groups in the cell supernatants and the cell lysates, respectively. Of these, 213 proteins in the cell supernatants (193 up-regulated and 20 down-regulated) and 564 in the cell lysates (358 up-regulated and 206 down-regulated) showed differential expression compared to control cells. Up-regulated proteins included TFPI, CD59, VWF, ANGPT2, MMRN1, and FLT1, which are involved in endothelial activation, angio-genesis, and coagulation regulation. Conversely, C3, SERPINE1, SERPINB2, PLAU, PLAUR, and ICAM1 were down-regulated, suggesting modulation of fibrinolysis, inflammation, and cell adhesion pathways. These findings indicate that adult A. vasorum homogenate induces a multifactorial endothelial activation characterized by dysregulation of coagulation, complement, and vascular remodelling pathways. Future studies focusing on the temporal and molecular characterization of endothelial responses to excretory/secretory antigens in both definitive and accidental hosts will further clarify the mechanisms of vascular pathology and parasite tolerance. Full article

Traumatic brain injury (TBI) can lead to persistent adverse outcomes, including cognitive and emotional dysfunction, with recent estimates indicating that up to 50% of individuals with mild TBI experience long-term symptoms. Growing evidence suggests that biological sex influences TBI outcomes and recovery trajectories; however, the molecular underpinnings driving these sex-specific differences remain poorly understood. In this study, a preclinical TBI model was used to directly compare chronic glutamatergic alterations in adult male and female Sprague Dawley rats. To define frontocortical molecular signatures associated with sex-specific glutamatergic dysfunction, proteomic analyses were conducted. Proteomic data revealed dysregulation of key pathways, cellular processes, and molecular regulators involved in excitatory signaling and synaptic function in both sexes. Biomarker profiling identified a single common biomarker between males and females, along with multiple biomarkers unique to each sex. Furthermore, two key brain regions highly susceptible to TBI, the prefrontal cortex and hippocampal subregions, were examined for chronic alterations in key glutamatergic signaling proteins, including N-methyl-D-aspartate (NMDA) receptors and the excitatory synaptic marker postsynaptic density protein 95 (PSD95). Immunofluorescence analyses revealed both sex- and region-specific alterations in the expression of NMDA receptor subunits, as well as in PSD95. Notably, many of these changes were concentrated within the hippocampal subregions, suggesting long-term dysregulation of hippocampal glutamatergic circuitry following injury. Together, these findings indicate the emergence of chronic sex-specific pathophysiology in glutamate signaling after TBI and highlight the importance of incorporating sex as a biological variable in the development of precision medicine-based therapeutic strategies for TBI. Full article

Feline conjunctivitis is a common ocular disorder; however, the molecular composition of feline tear fluid and its alterations during ocular surface inflammation remain poorly characterized. This pilot study aimed to explore the tear proteome of cats with conjunctivitis using matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI–TOF/TOF MS) and to compare findings with those from clinically healthy cats. Tear samples were collected using Schirmer tear test strips from healthy cats and cats diagnosed with conjunctivitis. Total protein concentration was measured by ultraviolet absorbance spectrophotometry, and tear proteins were separated by SDS–polyacrylamide gel electrophoresis, followed by in-gel trypsin digestion and MALDI–TOF/TOF MS analysis. Nine distinct tear proteins were identified, including antimicrobial and immune-related components such as lactoperoxidase, lactotransferrin, albumin, and immunoglobulin A constant region. Lactoperoxidase and SBP1 were identified in feline tear fluid for the first time. No proteins uniquely associated with conjunctivitis were detected. The mean total tear protein concentration was numerically higher in cats with conjunctivitis (13.06 ± 0.75 mg/mL) than in healthy cats (9.69 ± 0.67 mg/mL); however, this difference did not reach statistical significance (p = 0.095) and should be interpreted cautiously given the limited sample size. This pilot study provides preliminary insights into tear protein profiles in cats with conjunctivitis and highlights the need for larger quantitative investigations. These findings provide a preliminary framework for future studies aimed at further characterizing molecular alterations associated with feline ocular surface disorders. Full article

Background: Cartilage defects remain a clinical challenge due to the limited intrinsic repair capacity of hyaline cartilage, driving increasing interest in blood-derived products, including platelet-rich plasma (PRP). Variability in PRP preparation and activation protocols limits reproducibility and clinical translation, particularly in large animal models where species-specific differences are an additional cue. This study aimed to standardize and optimize in pigs a protocol for plasma rich in growth factors (PRGF), a leukocyte-poor PRP, aligned with current human clinical practice. Methods: Whole blood from six female pigs was processed via three centrifugation protocols and activated with varying CaCl₂ concentrations to evaluate gelation and morphology. PRGF was characterized through hematological analysis, ELISA-based quantification of soluble factors, and structural imaging of fibrin gel via histology and scanning electron microscopy. Data were further analyzed using protein–protein interaction networks, hierarchical clustering, and comparative human PRGF proteomic profiles. Results: Protocol with 400× g centrifugation followed by 13.3 mM CaCl₂ activation achieved the most favorable performance, yielding the highest platelet recovery, effective leukocyte clearance, and consistent formation of a well-organized fibrin network. Porcine activated PRGF showed substantial overlap in detected factors and concentration ranges with human activated PRGF prepared with the same protocol. Conclusions: These findings establish a robust, clinically aligned porcine PRGF protocol and support the pig as a relevant translational model for PRP-based regenerative strategies, providing a reliable platform for preclinical evaluation of cartilage therapies. Full article

Receptor protein tyrosine phosphatases (RPTPs) are transmembrane enzymes that counterbalance protein tyrosine kinase activity by catalyzing the removal of phosphate groups from tyrosine residues on target proteins. Despite their critical roles in regulating cellular proliferation, adhesion, differentiation, and survival, RPTPs remain significantly understudied compared to their kinase counterparts. Contrary to early assumptions that PTPs function as constitutive housekeeping enzymes, emerging evidence demonstrates that RPTPs exhibit highly context-dependent roles in cancer, functioning as tumor suppressors or tumor promoters, or displaying dual activities depending on tissue type, cellular environment, and the specific signaling networks involved. This review provides a comprehensive analysis of RPTP structure, catalytic mechanisms, regulatory processes, and interactions with signaling effectors in cancer. Through a systematic examination of RPTP expression patterns across ten cancer types using Clinical Proteomic Tumor Analysis Consortium (CPTAC) and International Cancer Proteogenome Consortium (ICPC) datasets, we identify subfamily-specific and cancer-type-specific expression alterations that correlate with established functional classifications. PTPσ and PTPμ emerge as uniformly downregulated tumor suppressors across diverse malignancies, whereas PTPα and PTPε display oncogenic potential by activating Src family kinases. Context-dependent RPTPs, such as LAR and DEP-1, exhibit variable expression patterns that reflect their complex, multifaceted signaling roles. These findings establish RPTPs as critical regulators of cancer signaling with significant therapeutic potential while underscoring the need to understand tissue-specific signaling architectures when developing RPTP-targeted interventions. Full article

Accurate prediction of submitochondrial localization is fundamental to understanding mitochondrial biogenesis and cellular metabolic pathways. While deep representations from pre-trained protein language models (pLMs) have significantly advanced the field, traditional global average pooling methods often fail to capture critical, localized N-terminal targeting signals, particularly in long sequences where these motifs are mathematically diluted. To resolve this “signal dilution” bottleneck, we developed a multi-scale architecture that explicitly integrates high-resolution N-terminal features with global evolutionary context derived from ESM-2 embeddings. The proposed framework utilizes an orthogonal mixing strategy consisting of Token-mixing and Channel-mixing. Token-mixing is specifically designed to detect spatial rhythmic patterns across residue positions, while Channel-mixing refines the biochemical signatures within the latent feature space. Extensive benchmarking across diverse datasets demonstrates that our approach effectively maintains signal integrity. Compared to existing state-of-the-art methods, the model achieves a superior overall Generalized Correlation Coefficient (GCC) of 0.7443 on the SM424-18 dataset and 0.7878 on the SubMitoPred dataset, outperforming the latest benchmarks by 9.4% and 16.1%, respectively. Furthermore, on the independent M983 test set, our method maintained a high GCC of 0.6945, demonstrating a 9.9% improvement relative to the state-of-the-art methods. This robust and efficient framework provides a high-precision tool for large-scale mitochondrial proteomics. Full article

Background/Objectives: Cholesterol is an essential lipid required for membrane structure and normal physiological functions. However, dysregulation of cholesterol homeostasis, manifesting as hypercholesterolemia, can precipitate a range of metabolic and cardiovascular diseases. Blautia species are important gut commensals, but their role in cholesterol metabolism remains poorly defined. Methods: A total of 63 Blautia strains isolated from human fecal samples were screened for cholesterol conversion using the o-phthalaldehyde colorimetric assay in cholesterol-containing media with or without oxgall. Cholesterol removal by live and heat-inactivated cells was compared. Metabolomic, transcriptomic, and proteomic analyses were employed to investigate molecular mechanisms and involved genes. Results: Nine strains significantly lowered cholesterol levels (live cells: 31–78%; heat-inactivated cells: 8–64%), with the B. hominis strain HA2291, the Blautia sp. strain HA3515, and the B. coccoides strain HA4419 showing the strongest activity. Oxgall increased cholesterol removal by live cells to 74–83%, indicating bile-tolerant metabolism activity. Metabolomic profiling revealed that B. hominis HA2291 transformed cholesterol into cholest-4-en-3-one and epicholestanol. An SCP2-like protein, RS03310, was identified as a candidate cholesterol-interacting factor; its recombinant form catalyzed measurable NAD⁺-dependent cholesterol oxidation in vitro. Conclusions: Blautia hominis HA2291 may employ multiple in vitro strategies for cholesterol-lowering, including cell-surface adsorption (heat-inactivated cells), bile-enhanced removal (oxgall effect), and enzymatic transformation, with the gene RS03310 implicated as the main contributor. These findings provide in vitro mechanistic insights into Blautia-mediated cholesterol metabolism, highlight RS03310 as a candidate gene associated with cholesterol biotransformation, and advance our understanding of the potential role of Blautia in host cholesterol homeostasis. 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

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

Taxifolin, a natural flavonoid, consistently exerts cytoprotective effects against various oxidative stresses. In this study, we systematically evaluated its photoprotective efficacy and underlying mechanisms against ultraviolet B (UVB)-induced injury in human immortalized keratinocytes (HaCaT). Cell viability and apoptosis were assessed by MTT, fluorescence staining, and flow cytometry, while integrative transcriptomic and proteomic analyses were employed to identify core pathways and key mediators. Taxifolin exhibited antioxidant capacity comparable to that of ascorbic acid under identical in vitro radical-scavenging assays. Moreover, it displayed a strong absorption peak at 289 nm that overlaps the UVB spectrum (280–320 nm), enabling it to act as a chemical sunscreen. In UVB-challenged HaCaT cells, taxifolin markedly reduced intracellular reactive oxygen species (ROS) and attenuated JNK/p38 MAPK activation, as evidenced by Western blot, thereby breaking the ROS-MAPK vicious cycle. Multi-omics revealed that taxifolin was associated with attenuation of UVB-imposed G1/S arrest concomitant with restored Cyclin expression, while up-regulating MYC, FOXQ1, HMOX1 and AP-1 components c-Jun/c-Fos and thereby switching on a pro-survival transcriptional program. Consequently, apoptosis was suppressed and survival was significantly improved. Collectively, taxifolin integrated chemical filtration, ROS scavenging and signaling modulation to support a multi-target photoprotective network, which provides mechanistic insight into taxifolin-mediated cytoprotection and identifies candidate molecular nodes for further validation. Full article

Antimicrobial resistance (AMR) remains a serious public health concern, and methicillin-resistant Staphylococcus aureus (MRSA) continues to limit treatment options. This laboratory-based comparative study evaluated antibiotic resistance patterns and nanoparticle (NP) susceptibility among 110 S. aureus isolates recovered from human skin and soft tissue infections (n = 80) and camel milk (n = 30). Proteomic identification utilizing matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was carried out for all isolates under study. Phenotypic differentiation between MRSA and methicillin-sensitive S. aureus (MSSA) was performed via the cefoxitin disk diffusion method, and antimicrobial susceptibility testing was carried out using the disk diffusion method as stated in international guidelines. Multidrug resistance (MDR) was defined by established criteria. The antibacterial activity of silver nanoparticles (AgNPs) and gold nanoparticles (AuNPs) was detected by broth microdilution to determine minimum inhibitory concentration values (MIC₅₀ and MIC₉₀). The ability to develop reduced susceptibility was evaluated through ten serial sub-inhibitory passages followed by stability testing without using nanoparticles. MRSA prevalence was 52.5% among human isolates and 70% among camel milk isolates. Overall, 56.4% of isolates met MDR criteria, with a significantly higher MDR rate among MRSA compared with MSSA. Both human and camel isolates showed similar resistance patterns. AgNPs exhibited strong antibacterial activity, with MIC₅₀ and MIC₉₀ values of 0.0078 mg/mL and 0.0156 mg/mL, respectively; nevertheless, AuNPs demonstrated higher MIC values. Response to NPs was similar between isolates, independent of methicillin resistance or MDR. Serial sub-inhibitory exposure resulted in increased MIC values in all tested isolates, and stable resistance persisted in 50% of cases. These results indicate ongoing MRSA circulation in human and animal settings and reinforce the need for careful and controlled use of NP-based antimicrobials. Full article

Gluten proteins are key components in wheat flour that determine the formation of dough and the quality of flour-based products. Upon hydration and mixing, gluten proteins undergo complex structural transformations to form a gluten network, exhibiting a hierarchical multi-scale structure spanning molecular, aggregate, and network scales. Due to the extreme complexity of gluten proteins, accurately characterizing their multi-scale structures remains challenging, requiring the combined application of multiple techniques, which are still relatively limited and thus warrant further exploration. Therefore, this review presents the principles, operational details, and result presentations of current techniques at different structural scales, including electrophoresis, high-performance liquid chromatography, proteomics, Fourier transform infrared spectroscopy, and Fourier transform Raman spectroscopy at the molecular scale; size-exclusion chromatography, asymmetrical flow field-flow fractionation, dynamic light scattering, multi-angle light scattering, differential refractive index, and ultraviolet absorbance at the aggregate scale; and confocal laser scanning microscopy, scanning electron microscopy, confocal Raman microscopy, and two-photon excitation microscopy at the network scale, among others. It further compares the advantages and disadvantages of similar techniques, facilitating their scenario-based selective utilization. Finally, it outlines the ongoing challenges and future perspectives for the development and application of techniques for the multi-scale structural characterization of gluten proteins. Full article