Search Results (9,136)

Malignant pleural mesothelioma (MPM) is a rare neoplasm with increasing incidence and mortality rates. Although recent advances have improved the overall prognosis, they have not had an important impact on survival of patients with MPM, such that more effective treatments are needed. Some species of marine snails have been demonstrated to be potential sources of novel anticancer molecules. This study analyzed the anticancer effects in vitro and in vivo of two peptides found in C. californicus. The effects of s-cal14.1b and s-cal14.2b on cell proliferation, apoptosis, and cytotoxicity were evaluated in 2D and 3D cultures of MPM-derived cells. Proteomics analysis of 3D cultures treated with conotoxins was performed to examine changes in expression or abundance. And the therapeutic effects of both conotoxins were evaluated in MPM mouse xenografts. s-cal14.1b and s-cal14.2b induced apoptosis and cytotoxicity in 2D and 3D cultures. However, only s-cal14.1b modified spheroid growth. Approximately 600 proteins exhibited important differential expression, which was more heterogeneous in H2452 vs MSTO-211H spheroids. The in silico protein functional analysis showed modifications in the biological pathways associated with carcinogenesis. CAPN1, LIMA1, ANXA6, HUWE1, PARP1 or PARP4 proteins could be potential cell targets for conotoxins and serve as biomarkers in MPM. Finally, we found that both conotoxins reduced the tumor mass in MPM xenografts; s-cal14.1b reached statistical significance. Based on these results, s-cal14.1b and s-cal14.2b conotoxins could be potential therapeutic drugs for MPM neoplasms with no apparent side effects on normal cells. Full article

Background: The proteomic analysis of serum extracellular vesicles (EVs) could be a useful tool for studying the pathophysiology of Crohn’s disease (CD) and ulcerative colitis (UC), as well as for biomarker discovery. Aims: To characterize the proteomic composition of serum EVs in patients with CD and UC to identify biomarkers and molecular pathways associated with pathogenesis and activity. Methods: Serum EVs were enriched and analyzed in patients with quiescent CD, active CD (aCD), quiescent UC, active UC (aUC), and healthy controls (HCs) (n = 30 per group). All groups were matched for age and sex. Disease activity was assessed by ileocolonoscopy and categorized based on the SES-CD (CD) and the endoscopic sub-score of the Mayo Score (UC). EVs were enriched by ultracentrifugation, and their size and concentration were determined by nanoparticle tracking analysis. The expression of CD63, CD81, and CD9 was determined using Western blotting. Proteomic analysis was performed by label-free nano-LC MS/MS. Results: A total of 324 proteins were identified; 60 showed differential abundance in CD-HC, 34 in UC-HC, and 21 in CD-UC. Regarding disease activity, the abundance of 58 and 32 proteins was altered in aCD-HC and aUC-HC, respectively. Functional analyses revealed that proteins associated with aCD were involved in immune regulation, whereas those linked to aUC were enriched in oxidative stress. Conclusions: We have identified expressed proteins between EVs from patients with CD and UC, depending on the presence of disease, the disease type, and the disease activity. These proteins are potential candidates as disease biomarkers and open new research avenues to better understand these conditions. Full article

Background/Objectives: Hepatocellular carcinoma (HCC) remains a significant global health concern, primarily due to the limited efficacy of targeted therapies, which are often compromised by drug resistance and adverse side effects. Methods: In this study, we utilized a Tandem Mass Tag (TMT)-based quantitative proteomic approach to analyze global protein expression and serine/threonine/tyrosine (S/T/Y) phosphorylation modifications in HepG2 cells following treatment with three clinically relevant hepatocellular carcinoma-targeted agents: apatinib, regorafenib, and lenvatinib. Results: Utilizing KEGG pathway enrichment analysis, biological process enrichment analysis, and protein interaction network analysis, we elucidated the common and specific metabolic pathways, biological processes, and protein interaction regulatory networks influenced by three liver cancer therapeutics. The study additionally proposed potential combinational treatment strategies, highlighting a possible synergistic interaction between HCC-targeted drugs and the DNA methyltransferase inhibitor. Furthermore, through the integration of clinical phosphorylation site data, we identified several phosphorylation sites that exhibited higher abundance in tumor tissues compared to adjacent non-tumor tissues. These sites were associated with poor prognosis and elevated functional scores. Conclusions: In summary, this study conducted an in-depth analysis of the molecular alterations in proteins and phosphorylation modifications induced by clinical HCC-targeted drugs, predicting drug combination strategies and therapeutic targets. Full article

Aflatoxin B1 (AFB1) and Ochratoxin A (OTA) are considered the most important mycotoxins in terms of food safety. The aim of this study was to evaluate the hepatotoxicity of AFB1 and OTA exposure in Wistar rats and to assess the beneficial effect of fermented whey (FW) and pumpkin (P) as functional ingredients through a proteomic approach. For the experimental procedures, rats were fed AFB1 and OTA individually or in combination, with the addition of FW or a FW-P mixture during 28 days. For proteomics analysis, peptides were separated using a LC-MS/MS-QTOF system and differentially expressed proteins (DEPs) were statistically filtered (p < 0.05) distinguishing males from females. Gene ontology visualization allowed the identification of proteins involved in important biological processes such as the response to xenobiotic stimuli and liver development. Likewise, KEGG pathway analysis reported the metabolic routes as the most affected, followed by carbon metabolism and biosynthesis of amino acids. Overall, the results highlighted a strong downregulation of DEPs in the presence of AFB1 and OTA individually but not with the mixture of both, suggesting a synergistic effect. However, FW and P have helped in the mitigation of processes triggered by mycotoxins. Full article

Pseudomonas aeruginosa and Mycobacterium abscessus are opportunistic pathogens that cause severe infections in hospitals, and their co-infections are increasingly reported. The interspecies interactions between these two bacterial species and their potential impacts on infections are largely unexplored. In this study, we first demonstrated that P. aeruginosa inhibits the growth of M. abscessus by iron chelating via pqs quorum sensing. Next, through proteomic analysis, we discovered that the PQS molecule significantly changed a large amount of protein expression in M. abscessus, including proteins involved in the type VII secretion system and iron homeostasis. Furthermore, we revealed that PQS significantly enhanced the production of bacterial membrane vesicles (MVs) by M. abscessus. Our study suggests that the P. aeruginosa PQS can serve as an interspecies signaling molecule to communicate with Mycobacterium and affect their physiology and virulence. Full article

Bisphenol A, an endocrine-disrupting compound, is widely used in the industrial production of plastic products. Despite increasing concerns about its harmful effects on human health, animals, and the environment, the use of BPA has been banned only in infant products, and its effects on cellular processes are not fully understood. To investigate the impact of BPA on eukaryotic cells, we analyzed the proteome changes of wild-type and PDR5-deleted S. cerevisiae strains exposed to different doses of BPA using sample multiplexing-based proteomics. We found that the ABC multidrug transporter Pdr5 plays an important role in protecting yeast cells from BPA toxicity, with its absence significantly sensitizing cells to BPA. BPA inhibited yeast growth in a dose-dependent manner, with a more pronounced effect in PDR5-deleted cells. Proteomic analysis revealed that BPA induces widespread dose-dependent changes in protein abundance, including the upregulation of metabolic pathways such as arginine biosynthesis and the downregulation of mitochondrial proteins. Additionally, we observed markers of cellular stress induced by BPA by identifying multiple stress-induced proteins that were upregulated by this compound. As cellular processes affected by BPA have been shown to be evolutionarily conserved, these insights can advance our understanding of BPA’s cellular impact and its broader effects on human health. Full article

Goldfish (Carassius auratus), subjected to millennia of artificial selection and breeding, have diversified into numerous ornamental varieties, such as the celestial-eye (CE) goldfish, noted for its unique dorsal eye rotation. Previous studies have primarily focused on anatomical modifications in CE goldfish eyes, yet the molecular underpinnings of their distinctive eye orientation remain poorly understood. This study employed high-throughput transcriptome and proteome sequencing on 110-day-old full-sibling CE goldfish, which displayed either anterior or upward eye rotations. Verification of these findings was conducted using quantitative PCR (qPCR) for transcriptomic data and parallel reaction monitoring (PRM) for proteomic analysis. Our research identified 73,685 genes and 7717 proteins, pinpointing 8 common differentially expressed genes (DEGs) and proteins (DEPs) implicated in cytoskeleton remodeling, cell adhesion, apoptosis, and optic nerve regeneration. Enrichment analyses further delineated pathways associated with apoptosis, necroptosis, and cell adhesion molecules. The results indicated a significant role for genes involved in cytoskeletal dynamics, nervous system function, and apoptotic processes in the dorsal eye rotation of CE goldfish. Analyses of abnormalities in ocular membrane structures, along with disturbances in lipid and protein synthesis metabolism and energy metabolism during developmental stages, provided compelling evidence for the potential use of CE goldfish as a model organism in studying human eye-related disorders. This investigation provided the first comprehensive transcriptomic and proteomic overview of eye rotation in CE goldfish, offering insights crucial for the genetic breeding of new ornamental fish varieties. Full article

Background: Polyunsaturated fatty acids in particular omega-3 fatty acids, such as docosahexaenoic acid (DHA), are essential nutrients and components of the plasma membrane. They are involved in various processes, including synaptic development, functionality, integrity, and plasticity, and are therefore thought to have general neuroprotective properties. Considerable research evidence further supports the beneficial effects of omega-3 fatty acids, specifically on mitochondria, through their antioxidant and anti-apoptotic properties, making them an attractive addition in treatment options for neurodegenerative disorders in which mitochondrial alterations are commonly observed. However, precise information on the underlying protective mechanisms is still lacking. Methods: We utilized the most common neuronal cell line (SH-SY5Y) and induced mitochondrial oxidative stress through the addition of rotenone. To study the potential protective effect of DHA, the cells were additionally pre-treated with DHA prior to rotenone administration. By combining SILAC labeling, mitochondria enrichment, and subsequent proteomic analyses, we aimed to determine the capacity of DHA to alleviate mitochondrial oxidative stress in vitro and further shed light on the molecular mechanisms contributing to the proposed neuroprotective effect. Results: We confirmed a reduced cell viability and an increased abundance of reactive oxygen species upon rotenone treatment, DHA pre-treatment was shown to decrease said species. Additionally proteomic analysis revealed an increased expression of mitochondrial proteins in DHA pre-treated cells. Conclusions: With our study, we were able to define a potential compensatory mechanism by which the inhibition of complex I is overcome by an increased activity of the fatty acid beta oxidation in response to DHA. Full article

Malignant peripheral nerve sheath tumors (MPNSTs) are rare but aggressive malignancies with a low 5-year survival rate despite current treatments. MPNSTs frequently harbor mutations in key genes such as NF1, CDKN2A, TP53, and PRC2 components (EED or SUZ12) across different disease stages. With the rapid advancement of high-throughput sequencing technologies, the molecular characteristics driving MPNST development are becoming clearer. This review summarizes recent sequencing studies on peripheral nerve sheath tumors, including plexiform neurofibromas (PNs), atypical neurofibromatous neoplasm with uncertain biologic potential (ANNUBP), and MPNSTs, highlighting key mutation events in tumor progression from the perspectives of epigenetics, transcriptomics, genomics, proteomics, and metabolomics. We also discuss the therapeutic implications of these genomic findings, focusing on preclinical and clinical trials targeting these alterations. Finally, we conclude that overcoming tumor resistance through combined targeted therapies and personalized treatments based on the molecular characteristics of MPNSTs will be a key direction for future treatment strategies. Full article

It is well known that individual pea (Pisum sativum L.) cultivars differ in their symbiotic responsivity. This trait is typically manifested with an increase in seed weights, due to inoculation with rhizobial bacteria and arbuscular mycorrhizal fungi. The aim of this study was to characterize alterations in the root proteome of highly responsive pea genotype k-8274 plants and low responsive genotype k-3358 ones grown in non-sterile soil, which were associated with root colonization with rhizobial bacteria and arbuscular mycorrhizal fungi (in comparison to proteome shifts caused by soil supplementation with mineral nitrogen salts). Our results clearly indicate that supplementation of the soil with mineral nitrogen-containing salts switched the root proteome of both genotypes to assimilation of the available nitrogen, whereas the processes associated with nitrogen fixation were suppressed. Surprisingly, inoculation with rhizobial bacteria had only a minor effect on the root proteomes of both genotypes. The most pronounced response was observed for the highly responsive k-8274 genotype inoculated simultaneously with rhizobial bacteria and arbuscular mycorrhizal fungi. This response involved activation of the proteins related to redox metabolism and suppression of excessive nodule formation. In turn, the low responsive genotype k-3358 demonstrated a pronounced inoculation-induced suppression of protein metabolism and enhanced diverse defense reactions in pea roots under the same soil conditions. The results of the study shed light on the molecular basis of differential symbiotic responsivity in different pea cultivars. The raw data are available in the PRIDE repository under the project accession number PXD058701 and project DOI 10.6019/PXD058701. Full article

Cell surface receptors are pivotal to cancer cell transformation, disease progression, metastasis, early detection, targeted therapy, drug responses, and clinical outcomes. Since they coordinate complex signaling communication networks in the tumor microenvironment, mapping the physical interaction partners of cell surface receptors in vivo is vital for understanding their roles, functional states, and suitability as therapeutic targets. Yet traditional methods like immunoprecipitation and affinity purification–mass spectrometry often fail to detect key but weak or transient receptor–protein interactions. Proximity labeling, a cutting-edge proteomics technology, addresses these technical challenges by enabling precise mapping of protein neighborhoods around a receptor target on the cell surface of cancer cells. This technique has been successfully applied in vitro and in vivo for proteomic mapping across various model systems. This review explores the fundamental principles, technologies, advantages, limitations, and applications of proximity labeling in cancer biology, focusing on mapping receptor microenvironments. By advancing mechanistic insights into cancer cell receptor signaling mechanisms, proximity labeling is poised to transform cancer research, improve targeted therapies, and illuminate avenues to overcome drug resistance. Full article

The most severe form of muscular dystrophy (MD), known as Duchenne MD (DMD), remains an incurable disease, hence the ongoing efforts to develop supportive therapies. The dysregulation of autophagy, a degradative yet protective mechanism activated when tissues are under severe and prolonged stress, is critically involved in DMD. Treatments that harness autophagic capacities therefore represent a promising therapeutic approach. Osmolytes are protective organic molecules that regulate osmotic pressure and cellular homeostasis and may support tissue-repairing autophagy. We therefore explored the effects of the osmolyte ectoine in the standard mouse model of DMD, the mdx, focusing on the autophagy-related proteome. Mice were treated with ectoine in their drinking water (150 mg/kg) or through daily intraperitoneal injection (177 mg/kg) until they were 5.5 weeks old. Hind limb muscles were dissected, and samples were prepared for Western blotting for protein quantification and for immunofluorescence for an evaluation of tissue distribution. We report changes in the protein levels of autophagy-related 5 (ATG5), Ser366-phosphorylated sequestosome 1 (SQSTM1), heat shock protein 70 (HSP70), activated microtubule-associated protein 1A/1B-light chain 3 (LC3 II) and mammalian target of rapamycin (mTOR). Most importantly, ectoine significantly improved the balance between LC3 II and SQSTM1 levels in mdx gastrocnemius muscle, and LC3 II immunostaining was most pronounced in muscle fibers of the tibialis anterior from treated mdx. These findings lend support for the further investigation of ectoine as a potential therapeutic intervention for DMD. Full article

Helicobacter pylori is a Gram-negative bacterium and human pathogen that is linked to various gastric diseases, including peptic ulcer disease, chronic gastritis, and gastric cancer. The filament of the H. pylori flagellum is surrounded by a membranous sheath that is contiguous with the outer membrane. Proteomic analysis of isolated sheathed flagella from H. pylori B128 identified the lipoprotein HP0135 as a potential component of the flagellar sheath. HP0135 is a small protein, with the mature HP0135 lipoprotein only 28 amino acid residues in length. Deletion of hp0135 in H. pylori B128 resulted in morphological abnormalities that included extensive formation of outer membrane vesicles and increased frequency of mini-cells. Introducing a plasmid-borne copy of hp0135 into the H. pylori Δhp0135 mutant suppressed the morphological abnormalities. The phenotype of the Δhp0135 mutant suggests HP0135 has roles in stabilizing the cell envelope and cell division. Full article

H. longicornis is used as an experimental animal model for the study of three-host ticks due to its special life cycle and easy maintenance in the laboratory and in its reproduction. The life cycle of H. longicornis goes through a tightly regulated life cycle to adapt to the changing host and environment, and these stages of transition are also accompanied by proteome changes in the body. Here, we used the isobaric tags for a relative and absolute quantification (iTRAQ) technique to systematically describe and analyze the dynamic expression of the protein and the molecular basis of the proteome of H. longicornis in seven differential developmental stages (eggs, unfed larvae, engorged larvae, unfed nymphs, engorged nymphs unfed adults, and engorged adults). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the differentially expressed proteins (DEPs) were used. In our study, A total of 2044 proteins were identified, and their expression profiles were classified at different developmental stages. In addition, it was found that tissue and organ development-related proteins and metabolism-related proteins were involved in different physiological processes throughout the life cycle through the GO and KEGG analysis of DEPs. More importantly, we found that the up-regulated proteins of engorged adult ticks were mainly related to yolk absorption, degradation, and ovarian development-related proteins. The abundance of the cuticle proteins in the unfed stages was significantly higher compared with those of the engorged ticks in the previous stages. We believe that our study has made a significant contribution to the research on H. longicornis, which is an important vector of SFTSV. In this study, we identified changes in the proteome throughout the H. longicornis development, and functional analysis highlighted the important roles of many key proteins in developmental events (ovarian development, the molting process, the development of midgut, the development and degeneration of salivary glands, etc.). The revelation of this data will provide a reference proteome for future research on tick functional proteins and candidate targets for elucidating H. longicornis development and developing new tick control strategies. Full article

Background/Objectives: Antibiotic-resistant bacteria are becoming a major challenge in human and veterinary medicine, as well as in food processing. Methods: In this study, the protein diversity in antibiotic-sensitive and -resistant strains of Staphylococcus aureus and Escherichia coli was investigated by exposing them to varying doses of gamma irradiation, with and without antibiotic presence. Changes in bacterial protein profiles were characterized using MALDI-TOF MS to reveal dose-dependent adaptations and potentiation effects under combined irradiation and antibiotic treatments. Results: The results indicate that MALDI-TOF MS effectively differentiates between sensitive and resistant strains, particularly at lower radiation doses (0, 0.2, and 0.4 kGy), with distinct separation in protein spectra. However, at 0.6 kGy, protein profiles plateaued, suggesting a potential threshold effect in radiation response. In 24-h cultures from irradiated Staphylococcus aureus, significant differences emerged in the resistant strain at 0.6 kGy in the presence of antibiotics, with further generational divergence dependent on initial antibiotic exposure. In the case of the sensitive strain, profiles were notably distinct at the 0.4 and 0.6 kGy doses, revealing dose- and treatment-specific responses. For Escherichia coli, generational differences between resistant and sensitive strains were apparent, though antibiotic effects on protein profiles were limited to the 0.6 kGy dose. Conclusions: The results underscore a potentiation interaction between irradiation and antibiotic exposure, affecting protein diversity and adaptation. Sensitive strains displayed heightened proteomic responses to minor treatment variations, while resistant strains exhibited more stable profiles across conditions. The findings highlight MALDI-TOF MS as a valuable tool in detecting proteomic biomarkers linked to bacterial resistance and stress adaptation. Full article