Search Results (326)

Flammulina filiformis, one of the most delicious and commercially important mushrooms, demonstrates remarkable adaptability to diverse agricultural wastes. However, it is unclear how different substrates affect the degradation of lignocellulosic biomass and the production of lignocellulolytic enzymes in F. filiformis. In this study, label-free comparative proteomic analysis of F. filiformis cultivated on sugarcane bagasse, cotton seed shells, corn cobs, and glucose substrates was conducted to identify degradation mechanism across various substrates. Label-free quantitative proteomics identified 1104 proteins. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis of protein expression differences were predominantly enriched in energy metabolism and carbohydrate metabolic pathways. Detailed characterization of carbohydrate-active enzymes among the identified proteins revealed glucanase (GH7, A0A067NSK0) as the key enzyme. F. filiformis secreted higher levels of cellulases and hemicellulases on sugarcane bagasse substrate. In the cotton seed shells substrate, multiple cellulases functioned collaboratively, while in the corn cobs substrate, glucanase predominated among the cellulases. These findings reveal the enzymatic strategies and metabolic flexibility of F. filiformis in lignocellulose utilization, providing novel insights for metabolic engineering applications in biotechnology. The study establishes a theoretical foundation for optimizing biomass conversion and developing innovative substrates using targeted enzyme systems. Full article

Accounting for 15–30% of colorectal cancer cases, the serrated pathway remains poorly characterized compared to the adenoma–carcinoma sequence. It involves sessile serrated lesions as precursors and is characterized by BRAF mutations (BRAF^V600E), CpG island hypermethylation, and microsatellite instability (MSI). Using label-free proteomics, we compared normal tissue margins from patients with diverticular disease, sessile serrated lesions, low-grade adenomas, and high-grade adenomas. We identified S100A14 as significantly overexpressed in sessile serrated lesions compared to low-grade adenomas, high-grade adenomas, and normal tissues. This overexpression was confirmed by immunohistochemical scoring in an independent cohort. Gene expression analyses of public datasets showed higher S100A14 expression in BRAF^V600E-mutated and MSI-H colorectal cancers compared to microsatellite stable BRAF^wt tumors. This finding was confirmed by immunohistochemical scoring in an independent colorectal cancer cohort. Furthermore, single-cell RNA sequencing analysis from the Human Colon Cancer Atlas revealed that S100A14 expression in tumor cells positively correlated with the abundance of tumoral CD8⁺ cytotoxic T cells, particularly the CD8⁺ CXCL13⁺ subset, known for its association with a favorable response to immunotherapy. Collectively, our results demonstrate for the first time that S100A14 is a potential biomarker of serrated neoplasia and further suggests its potential role in predicting immunotherapy responses in colorectal cancer. Full article

The effective suppression of inflammation using disease-modifying therapies is essential in the treatment of multiple sclerosis (MS). Anti-CD20 monoclonal antibodies are commonly used long-term as maintenance therapies, largely due to the lack of reliable biomarkers to guide dosing and evaluate treatment response. However, prolonged use increases the risk of infections and other immune-mediated side effects. The unique ability of brain-derived blood extracellular vesicles (EVs) to cross the blood–brain barrier and reflect the central nervous system (CNS) immune status has sparked interest in their potential as biomarkers. This study aimed to assess whether blood-derived L1CAM⁺ EVs could serve as biomarkers of treatment response to rituximab (RTX) in patients with relapsing-remitting MS (RRMS). Serum samples (n = 25) from the baseline (month 0) and after 6 months were analyzed from the RTX arm of the ongoing randomized clinical trial OVERLORD-MS (comparing anti-CD20 therapies in RRMS patients) and were compared with serum samples from healthy controls (n = 15). Baseline cerebrospinal fluid (CSF) samples from the same study cohort were also included. EVs from both serum and CSF samples were characterized, considering morphology, size, and concentration, using transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). The immunophenotyping of EV surface receptors was performed using flow cytometry with the MACSPlex exosome kit, while label-free quantitative proteomics of EV protein cargo was conducted using a proximity extension assay (PEA). TEM confirmed the presence of EVs with the expected round morphology with a diameter of 50–150 nm. NTA showed significantly higher concentrations of L1CAM⁺ EVs (p < 0.0001) in serum total EVs and EBNA1⁺ EVs (p < 0.01) in serum L1CAM⁺ EVs at baseline (untreated) compared to in healthy controls. After six months of RTX therapy, there was a significant reduction in L1CAM⁺ EV concentration (p < 0.0001) and the downregulation of TNFRSF13B (p = 0.0004; FC = −0.49) in serum total EVs. Additionally, non-significant changes were observed in CD79B and CCL2 levels in serum L1CAM⁺ EVs at baseline compared to in controls and after six months of RTX therapy. In conclusion, L1CAM⁺ EVs in serum showed distinct immunological profiles before and after rituximab treatment, underscoring their potential as dynamic biomarkers for individualized anti-CD20 therapy in MS. Full article

This study aimed to investigate the underlying mechanisms by which dandelion extract inhibits the proliferation of breast cancer MDA-MB-231 cells. Dandelion root and leaf extracts were prepared using a heat reflux method and subjected to solvent gradient extraction to obtain fractions with different polarities. MTT assays revealed that the ethyl acetate fraction exhibited the strongest inhibitory effect on cell proliferation. LC-MS analysis identified 12 potential active compounds, including sesquiterpenes such as Isoalantolactone and Artemisinin, which showed significantly lower toxicity toward normal mammary epithelial MCF-10A cells compared to tumor cells (p < 0.01). Mechanistic studies demonstrated that the extract induced apoptosis in a dose-dependent manner, with an apoptosis rate as high as 85.04%, and significantly arrested the cell cycle at the S and G2/M phases. Label-free quantitative proteomics identified 137 differentially expressed proteins (|FC| > 2, p < 0.05). GO enrichment analysis indicated that these proteins were mainly involved in cell cycle regulation and apoptosis. KEGG pathway analysis revealed that the antitumor effects were primarily mediated through the regulation of PI3K-Akt (hsa04151), JAK-STAT (hsa04630), and PPAR (hsa03320) signaling pathways. Moreover, differential proteins such as PI3K, AKT1S1, SIRT6, JAK1, SCD, STAT3, CASP8, STAT2, STAT6, and PAK1 showed strong correlation with the core components of the EA-2 fraction of dandelion. Molecular docking results demonstrated that these active compounds exhibited strong binding affinities with key target proteins such as PI3K and JAK1 (binding energy < −5.0 kcal/mol). This study elucidates the multi-target, multi-pathway synergistic mechanisms by which dandelion extract inhibits breast cancer, providing a theoretical basis for the development of novel antitumor agents. Full article

Zebrafish (Danio rerio) combine accessible behavioral phenotypes with conserved neurochemical pathways and molecular features of vertebrate brain function, positioning them as a powerful model for investigating early neurodegenerative processes and screening neuroprotective strategies. In this context, integrated behavioral and proteomic analyses provide valuable insights into the initial pathophysiological events shared by conditions such as Parkinson’s disease and related disorders—including mitochondrial dysfunction, oxidative stress, and synaptic impairment—which emerge before overt neuronal loss and offer a crucial window to understand disease progression and evaluate therapeutic candidates prior to irreversible damage. To investigate this early window of dysfunction, zebrafish larvae were exposed to 500 μM 1-methyl-4-phenylpyridinium (MPP⁺) from 1 to 5 days post-fertilization and evaluated through integrated behavioral and label-free proteomic analyses. MPP⁺-treated larvae exhibited hypokinesia, characterized by significantly reduced total distance traveled, fewer movement bursts, prolonged immobility, and a near-complete absence of light-evoked responses—mirroring features of early Parkinsonian-like motor dysfunction. Label-free proteomic profiling revealed 40 differentially expressed proteins related to mitochondrial metabolism, redox regulation, proteasomal activity, and synaptic organization. Enrichment analysis indicated broad molecular alterations, including pathways such as mitochondrial translation and vesicle-mediated transport. A focused subset of Parkinsonism-related proteins—such as DJ-1 (PARK7), succinate dehydrogenase (SDHA), and multiple 26S proteasome subunits—exhibited coordinated dysregulation, as visualized through protein–protein interaction mapping. The upregulation of proteasome components and antioxidant proteins suggests an early-stage stress response, while the downregulation of mitochondrial enzymes and synaptic regulators reflects canonical PD-related neurodegeneration. Together, these findings provide a comprehensive functional and molecular characterization of MPP⁺-induced neurotoxicity in zebrafish larvae, supporting its use as a relevant in vivo system to investigate early-stage Parkinson’s disease mechanisms and shared neurodegenerative pathways, as well as for screening candidate therapeutics in a developmentally responsive context. Full article

Fatty liver is a major metabolic disease in periparturient dairy goats. Protein ubiquitination, a type of dynamic and multifaceted post-translational modification, plays an important role in metabolism by regulating the stability and function of target proteins. However, the hepatic protein ubiquitination profile in dairy goats with fatty liver is yet to be elucidated. In this study, we collected liver and blood samples from healthy dairy goats (Con, n = 3) and dairy goats with fatty liver (FL, n = 3). Then, we analyzed the overall ubiquitination of hepatic proteins in dairy goats with fatty liver through quantitative ubiquitin label-free proteomics and bioinformatics. Proteins showing significantly altered levels of ubiquitination were identified via bioinformatics, and related regulatory pathways were screened. The results showed that the blood levels of beta-hydroxybutyric acid and non-esterified fatty acids were significantly upregulated in dairy goats with fatty liver, and a total of 238 ubiquitination sites across 921 proteins were found to be differentially altered in the fatty liver group. Among them, ubiquitination was upregulated at 351 sites across 93 proteins and downregulated at 570 sites across 145 proteins. In addition, GO and KEGG pathway analysis revealed that the differentially ubiquitinated proteins were enriched in pathways regulating lipid metabolism, such as the PPAR signaling pathway, fatty acid degradation, and peroxisome activity. Notably, by observing the overlap among these three sub-networks, we found that proteins with downregulated ubiquitination—such as ACSL1, ACSL5, EHHADH, and ACAA1—were transcriptionally upregulated in dairy goats with fatty liver. This study reveals the key ubiquitinated proteins in dairy goats with fatty liver and provides a more comprehensive understanding of the pathogenesis of fatty liver in dairy goats. Full article

This study aims to investigate the effect of the Pd(II) complex on HeLa cells using computational biology and proteomic analysis. [Pd(dach)Cl₂]-treated HeLa cells were subjected to comparative proteomics analysis using label-free data-independent liquid chromatography-tandem mass spectrometry (LC-MS/MS). In parallel, the informational spectrum method (ISM) was used to predict potential protein interactors of the [Pd(dach)Cl₂] complex in HeLa cells. Proteomics analysis revealed 121 differentially abundant proteins (DAPs). Enrichment analysis of Gene Ontology (GO) annotations revealed ATP hydrolysis and RNA/protein binding as the top molecular functions and RNA splicing and protein–RNA complex organization as the top biological processes. Enrichment analysis of altered canonical pathways pointed out spliceosome and ribosome pathways. The top hub proteins with potential regulatory importance encompassed ribosomal proteins, translational and transcriptional factors, and components of the ribosome assembly machinery. ISM and cross-spectral analysis identified the nucleoplasm and sensor of the single-stranded DNA (SOSS DNA) complex. Proteome analysis showed that [Pd(dach)Cl₂] targets proteins involved in ribosomal biogenesis and RNA splicing, whereas theoretical prediction implies also potential effect on p53 signaling pathway, and thus, alterations of the expression of regulatory proteins involved in cell survival and proliferation. These findings underscore the potential of Pd(II) complexes as anti-cancer agents, warranting further exploration and detailed functional validation. Full article

Nasopharyngeal carcinoma (NPC) is a multifactorial disease mainly affecting the Southeast Asian and North African populations. Critically, there is a dearth of available circulating biomarkers for NPC. Additionally, as of this writing, there have been no prior plasma proteomics studies on NPC in the Moroccan population. Accordingly, there has been no integrated analysis of tumor and plasma for NPC in the Moroccan sub-population. Label-free proteomics analysis was conducted on 25 samples of Moroccan origin (10 NPC samples and 15 healthy control samples). Each sample was depleted of albumin, fractionated into eight fractions, and then analyzed using Liquid Chromatography–Tandem Mass Spectrometry (LC-MS/MS). A total of 291 proteins and 2702 unique peptides were identified across all samples. In total, 16 proteins were differentially expressed (DEPs) between NPC cases and healthy individuals. Of these, three showed prognostic significance, while four demonstrated diagnostic potential. A pathway analysis showed significantly enriched terms related to the immune response and chronic inflammation, revealing acute-phase proteins as differentially expressed. The investigation of patients with early and advanced stages of NPC revealed two DEPs, while four additional DEPs were identified across the three defined clusters of NPC. Across all comparisons, DEPs, such as H2A, IGHG2, SERPINA3, SAA1, CRP, PIGR, and APOA2, have shown potential as biomarkers for NPC, with several being identified for the first time. We additionally compared the plasma proteomic profile of NPC with the tumor proteomic profile, highlighting that deeper proteomics analysis of plasma may be required to quantify additional putative biomarkers that may be shed from the tumor into the blood. Our research presents the first plasma proteomic profile of NPC in Morocco and North Africa, identifying proteins that might ultimately have diagnostic and prognostic potential. Full article

Recent studies on myogenic satellite cells (SCs) in Duchenne muscular dystrophy (DMD) documented altered division capacities and impaired regeneration potential of SCs in DMD patients and animal models. It remains unknown, however, if SC-intrinsic effects trigger these deficiencies at pre-contractile stages of myogenesis rather than resulting from the pathologic environment. In this study, we isolated SCs from a porcine DMD model and age-matched wild-type (WT) piglets for comprehensive analysis. Using immunofluorescence, differentiation assays, traction force microscopy (TFM), RNA-seq, and label-free proteomic measurements, SCs behavior was characterized, and molecular changes were investigated. TFM revealed significantly higher average traction forces in DMD than WT SCs (90.4 ± 10.5 Pa vs. 66.9 ± 8.9 Pa; p = 0.0018). We identified 1390 differentially expressed genes and 1261 proteins with altered abundance in DMD vs. WT SCs. Dysregulated pathways uncovered by gene ontology (GO) enrichment analysis included sarcomere organization, focal adhesion, and response to hypoxia. Multi-omics factor analysis (MOFA) integrating transcriptomic and proteomic data, identified five factors accounting for the observed variance with an overall higher contribution of the transcriptomic data. Our findings suggest that SC impairments result from their inherent genetic abnormality rather than from environmental influences. The observed biological changes are intrinsic and not reactive to the pathological surrounding of DMD muscle. Full article

Serratia plymuthica, isolated from the midgut of Aedes aegypti, displays remarkable resilience to hemin, a toxic hemoglobin byproduct generated during blood digestion. This study explores its proteomic adaptations under oxidative stress induced by 5 mM hemin, mimicking midgut conditions. Growth assays demonstrated that S. plymuthica tolerated hemin concentrations ranging from 5 µM to 1 mM, reaching the stationary phase within approximately 10 h. Colonies exhibited morphological changes—darkened peripheries and translucent halos—suggesting heme accumulation and detoxification. Label-free quantitative proteomics identified 436 proteins, among which 28 were significantly upregulated—including universal stress proteins (USPs), ABC transporters, and flavodoxin—while 54 were downregulated, including superoxide dismutase and several ribosomal proteins. Upregulated proteins were associated with antioxidant defense, heme transport, and redox regulation, whereas downregulated proteins suggested metabolic reprogramming to conserve energy under stress. Functional enrichment analysis revealed significant alterations in transmembrane transport, oxidative stress response, and central metabolism. These findings suggest that S. plymuthica contributes to redox homeostasis in the mosquito gut by mitigating reactive oxygen species (ROS) and detoxifying excess heme, supporting its role as a beneficial symbiont. The observed stress tolerance mechanisms may influence mosquito physiology and vector competence, offering novel insights into mosquito–microbiota interactions and potential microbiota-based strategies for vector control. Full article

Microbial contamination is the leading cause of foodborne diseases and spoilage in food and personal care products. Previous studies by our group have demonstrated that vine tea extract (VTE) and dihydromyricetin (DMY) inhibit the growth of Escherichia coli. In this study, we further explored the inhibitory mechanisms of VTE and DMY against E. coli through a label-free proteomics approach. The proteomic analysis detected 130 and 81 differentially expressed proteins (DEPs) in E.coli following VTE and DMY treatment, respectively. The analysis indicated that VTE and DMY inhibit bacterial growth through multiple-target mechanisms. Specifically, they inhibit E. coli growth by disrupting the cationic antimicrobial peptide resistance pathway, amino acid biosynthesis and metabolism, and nucleotide metabolism. Additionally, VTE disrupts various secondary metabolic pathways, while DMY interferes with E. coli ribosome assembly and function, and disrupts cell membrane lipid homeostasis by interfering with fatty acid metabolism. RT-qPCR validation confirmed transcriptional alterations in genes encoding key target proteins. Molecular docking results indicated that DMY may affect bacterial protein synthesis, cationic antimicrobial peptide resistance, and transcriptional regulation by binding to target proteins such as RplB, RplV, LpxA, and YafC. In conclusion, this study systematically deciphered the multi-target inhibitory mechanisms of VTE and DMY against E. coli, providing a theoretical basis for developing plant-derived antimicrobial agents. Full article

This study investigated the role of exosomes in the pathological processes of gouty arthritis (GA), with the aim of clarifying their mechanistic role and pathological significance in the onset and progression of GA. Using a rat model of GA established through potassium oxonate and yeast gavage combined with intra-articular monosodium urate (MSU) injection, we isolated and characterized plasma exosomes using transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), and Western blotting. Differential exosomal protein expression was analyzed using 4D label-free proteomics technology, followed by GO and KEGG enrichment analyses, and protein–protein interaction (PPI) network construction to identify core targets. In vivo experiments measured the expression levels of CTSD in synovial tissues and joint fluid, as well as HPRT1 in renal tissues, while in vitro experiments involved co-culturing NRK cells with exosomes to validate target protein expression. The results indicated that serum uric acid levels were significantly elevated in the model group (p < 0.01), accompanied by pronounced joint swelling and inflammation. Exosome characterization confirmed their typical bilayer membrane structure and the expression of marker proteins (CD63/TSG101). Proteomic analysis identified 40 differentially expressed proteins (12 upregulated and 28 downregulated) enriched in pathways such as complement and coagulation cascades, autophagy, lysosomal function, and purine metabolism. In vivo and in vitro experiments demonstrated significantly increased CTSD expression (p < 0.05/p < 0.01) and decreased HPRT1 expression (p < 0.05/p < 0.01) in the model group, suggesting that exosomes are involved in the occurrence and development of GA by regulating purine metabolism and lysosomal dysfunction. These findings offer new insights into disease mechanisms and potential therapeutic targets. Full article

Background: Deinococcus radiodurans, renowned for its exceptional resistance to radiation, provides a robust model for elucidating cellular stress responses and DNA repair mechanisms. Previous studies have established PprI as a key regulator contributing to radiation resistance through its involvement in DNA damage repair pathways, oxidative stress response, and metabolic regulation. Methods: Building upon these foundations, our study employs label-free quantitative (LFQ) proteomics coupled with high-resolution mass spectrometry to systematically map pprI deletion protein networks by comparing the global proteomic profiles of pprI knockout and wild-type D. radiodurans strains. Results: Under stringent screening criteria, we identified 719 significantly higher and 281 significantly lower abundant proteins in the knockout strain compared to wild-type strains. Functional analysis revealed that PprI deficiency disrupts homologous recombination (HR) repair, activates nucleotide excision repair (NER) and base excision repair (BER) as a compensatory mechanism, and impairs Mn/Fe homeostasis and carotenoid biosynthesis, leading to increased oxidative stress. Furthermore, PprI deficiency induces significant metabolic reprogramming, including impaired purine synthesis, compromised cell wall integrity, etc. Conclusions: These proteomic findings delineate the extensive regulatory network influenced by PprI, revealing coordinated perturbations across multiple stress response systems when PprI is absent. Full article

Because soybean is sensitive to salt stress, it is necessary to improve their stress tolerance. Titanium-oxide nanoparticles (TiO₂ NPs) enhanced the growth of soybean under salt stress. To elucidate the promotive effects of TiO₂ NPs on soybean growth under salt stress, a gel-free/label-free proteomic analysis was carried out. The principal component analysis of proteins showed that TiO₂ NPs affected proteins in roots grown under salt stress. The differentially changed proteins were associated with protein metabolism and transport in the biological process, the nucleus in the cellular component, and nucleic acid binding activity in the molecular function. Proteins identified with proteomics were verified using immunoblot analysis. The abundance of V-ATPase decreased in soybean under salt stress and increased with additional TiO₂ NPs under stress, whereas xyloglucan endotransglucosylase/hydrolase did not change with any treatment. The abundance of peroxiredoxin increased under salt stress but decreased with additional TiO₂ NPs under stress. These results suggest that TiO₂ NPs confer salt tolerance in soybean plants at the early growth stage by regulating vacuole transport and reactive oxygen scavenging systems. Full article

Background/Objective: Anti-tick vaccines represent a promising alternative to chemical acaricides for the management of ticks on wildlife; however, little progress has been made to produce a vaccine effective in wild hosts that are critical for tick reproduction, such as the white-tailed deer (Odocoileus virginianus). We recently tested Amblyomma americanum salivary and midgut extracellular vesicles as vaccine candidates in white-tailed deer, which resulted in on-host female tick mortality. The objective of this study was to identify the proteins recognized by the antibodies regenerated during these vaccinations to determine potential antigens for vaccine development for white-tailed deer. Methods: Using a proteomic approach, we characterized the cargo within salivary and midgut vesicles. Label-free quantitative proteomics were used to investigate significant changes in protein loading within extracellular vesicles in these two organs. The pre-vaccination and post-vaccination serum from three animals vaccinated with salivary and midgut vesicles and one control animal were used to identify proteins recognized by circulating antibodies. Results: We show that these salivary and midgut vesicles contain a “core-cargo” enriched in chaperones, small GTPases, and other proteins previously reported in small EVs. Label-free quantitative proteomics show significant differences in protein cargo between salivary and midgut vesicles (333 proteins out of 516). Proteomic analysis of immunoprecipitated proteins identified thirty antigens with potential for use in anti-tick vaccines, seven of which we have categorized as high priority. Conclusions: Proteins within tick salivary and midgut vesicles are recognized by antibodies from vaccinated white-tailed deer. These proteins can be further evaluated for their function and potential as vaccine candidates against ticks. Full article