Search Results (112)

Background/Objectives: Oxidative stress constitutes a principal pathophysiological mechanism driving neurodegeneration and brain aging. α-Ketoglutarate (AKG), a key intermediate of the tricarboxylic acid (TCA) cycle, has shown potential in longevity and oxidative stress resistance. However, the role of AKG in oxidative stress-induced neuronal senescence and its interaction with the mTOR signaling pathway during neuronal aging remain poorly understood, posing a key challenge for developing senescence-targeted therapies. Methods: We investigated the neuroprotective effects of AKG using H₂O₂-induced senescence in HT22 cells and a D-galactose-induced brain aging mouse model. Assessments encompassed SA-β-gal staining, EdU incorporation, mitochondrial membrane potential (JC-1), and ROS measurement. Antioxidant markers, ATP levels, and the NAD⁺/NADH ratio were also analyzed. Proteomic profiling (DIA-MS) and KEGG/GSEA enrichment analyses were employed to identify AKG-responsive signaling pathways, and Western blotting validated changes in mTOR signaling and downstream effectors. Results: AKG significantly alleviated H₂O₂-induced senescence in HT22 cells, evidenced by enhanced cell viability, reduced ROS level, restored mitochondrial function, and downregulated p53/p21 expression. In vivo, AKG administration improved cognitive deficits and vestibulomotor dysfunction while ameliorating brain oxidative damage in aging mice. Proteomics revealed mTOR signaling pathways as key targets for AKG’s anti-aging activity. Mechanistically, AKG suppressed mTOR phosphorylation and activated ULK1, suggesting modulation of autophagy and metabolic homeostasis. These effects were accompanied by enhanced antioxidant enzyme activities and improved redox homeostasis. Conclusions: Our study demonstrates that AKG mitigates oxidative stress-induced neuronal senescence through suppression of the mTOR pathway and enhancement of mitochondrial and antioxidant function. These findings highlight AKG as a metabolic intervention candidate for age-related neurodegenerative diseases. Full article

Panton–Valentine leukocidin (PVL) is a pore-forming toxin secreted by Staphylococcus aureus (S. aureus) and a significant virulence factor that plays a crucial role in the pathogenesis of dairy mastitis. Previous studies by our research group demonstrated that baicalin inhibits the apoptosis and hyperphosphorylation of cytoskeletal proteins induced by recombinant Panton–Valentine leukocidin (rPVL) in bovine mammary epithelial cells (BMECs). However, the effects of baicalin on the proliferation of BMECs and the underlying mechanism remain unclear. Consequently, this study aimed to explore this underlying mechanism through an LC-MS/MS analysis performed in 4D data-independent acquisition (DIA) mode. Quantitative analysis identified 757 differentially expressed phosphoproteins, among which phosphorylation levels of proteins involved in BMEC proliferation and cell cycle regulation exhibited significant alterations (p < 0.05). rPVL inhibited BMEC proliferation in a dose-dependent manner and induced G0/G1 phase arrest and dephosphorylation of the cell-cycle-related proteins BCLAF1^S285, CDK7^T170, NF2^S518, and PKM2S37. Preintervention with baicalin significantly upregulated the expression and phosphorylation of these proteins and alleviated the G0/G1 phase arrest induced by rPVL in BMECs in vitro. The establishment of the mitotic state in BMECs due to the effect of baicalin appears to be closely related to the regulation of the phosphorylation of CDK7, PKM2, BCLAF1, and NF2. Moreover, in vivo analysis revealed that S. aureus ATCC49775 and rPVL induced dramatic structural destruction and pathological impairment of mammary gland tissues in mice and that these histopathological changes were ameliorated after baicalin intervention. Quantitative immunohistochemical analysis revealed that baicalin mitigated the rPVL-induced dephosphorylation of the aforementioned cell-cycle-related proteins and increased their phosphorylation. Both in vitro and in vivo experimental evidence demonstrated that baicalin effectively reversed rPVL-induced G0/G1 phase arrest in BMECs (p < 0.01) by significantly increasing the phosphorylation levels of cell cycle regulatory proteins (p < 0.05). Additionally, baicalin alleviates pathological damage to mammary gland tissues in mouse models. These data suggest that baicalin possesses antibacterial and antitoxin effects, indicating that it is an effective preventive agent against bovine mastitis. Full article

Tonsils are secondary lymphoid organs that play a crucial role in the immunological response, with B cells being a major component involved in both innate and adaptive immunity. Periodic fever, aphthous stomatitis, pharyngitis, and adenitis (PFAPA) syndrome and obstructive sleep apnea syndrome (OSAS) are both common pediatric conditions involving tonsillar pathology. In both syndromes, the molecular pathways dysregulated in tonsillar B cells are still to be understood. The study aimed to unravel and compare the proteomic profiles of tonsillar CD19+ B cells isolated from pediatric patients with PFAPA (n = 6) and OSAS (n = 6) to identify disease-specific molecular signatures. B cells were isolated from the tonsillar tissue using magnetic microbeads (with a purity of 93.50%). Proteomic analysis was performed by nanoLC-MS/MS with both data-dependent (DDA) and data-independent acquisition (DIA) methods, followed by comprehensive bioinformatic analysis. By merging DDA and DIA datasets, a total of 18.078 unique proteins were identified. Differential expression analysis revealed 83 proteins increased and 49 proteins decreased in OSAS B cells compared to PFAPA B cells (fold change ≥ 1.5 or ≤0.6, p < 0.05). Distinct pathway enrichments were highlighted, including alterations in the regulation of PTEN gene transcription, circadian gene expression, inflammasome pathways (IPAF and AIM2), and the metabolism of angiotensinogen to angiotensin. Specific proteins such as p53, Hdac3, RPTOR, MED1, Caspase-1, Cathepsin D, Chymase, and TLR2 (validated by WB) were shown to be differentially expressed. These findings reveal distinct proteomic signatures in tonsillar B cells from patients with PFAPA and OSAS, offering novel insights into the pathophysiology and potential avenues for biomarker discovery. Full article

Background: The reproductive ability of equine species is a critical component of equine breeding programs, with sperm quality serving as a primary determinant of reproductive success. In this study, we perform an integrative analysis of proteomics and metabolomics in seminal plasma to identify proteins and metabolites associated with sperm quality and reproductive ability in equine species. Methods: We utilized the CEROS instrument to assess the morphology and motility of sperm samples from three horses and three donkeys. Additionally, we statistically analyzed the mating frequency and pregnancy rates in both species. Meanwhile, the 4D-DIA high-throughput proteomic and metabolomic profiling of seminal plasma samples from horses and donkeys revealed a complex landscape of proteins and metabolites. Results: Our findings reveal a certain degree of correlation between seminal plasma proteins and metabolites and sperm quality, as well as overall fertility. Notably, we found that the proteins B3GAT3, XYLT2, CHST14, HS2ST1, GLCE, and HSPG2 in the glycosaminoglycan biosynthesis signaling pathway; the metabolites D-glucose, 4-phosphopantetheine, and 4-hydroxyphenylpyruvic acid in the tyrosine metabolism, starch, and source metabolisms; and pantothenate CoA biosynthesis metabolism present unique characteristics in the seminal plasma of equine species. Conclusions: This comprehensive approach provides new insights into the molecular mechanisms underlying sperm quality and has identified potential proteins and metabolites that could be used to indicate reproduction ability. The findings from this study could be instrumental in developing novel strategies to enhance equine breeding practices and reproductive management. Future research will focus on exploring their potential for clinical application in the equine industry. Full article

Background: Type 2 diabetes mellitus (T2DM) is an epidemic chronic disease that affects millions of people worldwide. This study aims to explore the impact of T2DM on the tear proteome, specifically investigating whether alterations occur before the development of diabetic retinopathy. Methods: Flush tear samples were collected from healthy subjects and subjects with preDM and T2DM. Tear proteins were processed and analyzed by mass spectrometry-based shotgun proteomics using a data-independent acquisition parallel acquisition serial fragmentation (diaPASEF) approach. Machine learning algorithms, including random forest, lasso regression, and support vector machine, and statistical tools were used to identify potential biomarkers. Results: Machine learning models identified 17 proteins with high importance in classification. Among these, five proteins (cystatin-S, S100-A11, submaxillary gland androgen-regulated protein 3B, immunoglobulin lambda variable 3–25, and lambda constant 3) exhibited differential abundance across these three groups. No correlations were identified between proteins and clinical assessments of the ocular surface. Notably, the 17 important proteins showed superior prediction accuracy in distinguishing all three groups (healthy, preDM, and T2DM) compared to the five proteins that were statistically significant. Conclusions: Alterations in the tear proteome profile were observed in adults with preDM and T2DM before the clinical diagnosis of ocular abnormality, including retinopathy. Full article

Understanding the mechanisms of protein preservation in extreme environments is essential for identifying potential molecular biosignatures on Mars. In this study, we investigated five sabkha sedimentary samples from the Abu Dhabi coast, spanning from the present day to ~11,000 years before present (BP), to assess how mineralogy and environmental conditions influence long-term protein stability. Using LC-MS/MS and direct Data-independent Acquisition (DIA) proteomic analysis, we identified 722 protein groups and 1300 peptides, revealing a strong correlation between preservation and matrix composition. Carbonate- and silica-rich samples favored the retention of DNA-binding and metal-coordinating proteins via mineral–protein interactions, while halite- and gypsum-dominated facies showed lower recovery due to extreme salinity and reduced biomass input. Functional profiling revealed a shift from metabolic dominance in modern samples to genome maintenance strategies in ancient ones, indicating microbial adaptation to prolonged environmental stress. Contrary to expectations, some ancient samples preserved large, multi-domain proteins, suggesting that early mineral encapsulation can stabilize structurally complex biomolecules over millennial timescales. Taxonomic reconstruction based on preserved proteins showed broad archaeal diversity, including Thaumarchaeota and thermophilic lineages, expanding our understanding of microbial ecology in hypersaline systems. These findings highlight sabkhas as valuable analogs for Martian evaporitic environments and suggest that carbonate–silica matrices on Mars may offer optimal conditions for preserving ancient molecular traces of life. Full article

The objective of this study was to elucidate the proteomic and transcriptomic alterations within the cartilage in Kashin–Beck disease (KBD) compared to a normal control. We conducted a comparison of the expression profiles of proteins, mRNAs, and lncRNAs via data-independent acquisition (DIA) proteomics and transcriptome sequencing in six KBD individuals and six normal individuals. To facilitate the functional annotation enrichment analysis of the differentially expressed (DE) proteins, DE mRNAs, and DE lncRNAs, we employed bioinformatic analysis utilizing Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Additionally, we conducted integration analysis of multi-omics datasets using mixOmics. We revealed a distinct proteomic signature, highlighting 53 DE proteins, with notable alterations in the pathways related to tryptophan metabolism and microbial metabolism. Additionally, we identified 160 DE mRNAs, with the functional enrichment analysis uncovering pathways related to RNA metabolism and protein splicing. Furthermore, our analysis of the lncRNAs demonstrated biological processes involved in protein metabolism and cellular nitrogen compound metabolic processes. The integrative analysis uncovered significant correlations, including the positive correlation between superoxide dismutase 1 (SOD1) and mitochondrial import receptor subunit TOM6 homolog (TOMM6), and the negative correlation between C-X9-C motif-containing 1 (CMC1) and succinate–CoA ligase [GDP-forming] subunit beta, mitochondrial (SUCLG2). Our results provide novel insights into the molecular mechanisms underlying KBD. Full article

Horses and donkeys, as integral members of the equine family, exhibit distinct reproductive capabilities and characteristics. Seminal plasma, the fluid component of semen, contains a variety of proteins that play critical roles in sperm function and fertility. This study aimed to systematically compare the protein profiles in the seminal plasma of horses and donkeys, thereby elucidating the molecular differences between these two species. The study utilized 4D-DIA proteomics technology to analyze seminal plasma from horses and donkeys and further validated key proteins through Western blot. Our findings revealed significant variations in seminal plasma protein composition between horses and donkeys. We identified 2380 and 2385 proteins in the seminal plasma of horses and donkeys. Among these proteins, 59 are solely present in the seminal plasma of horses, and 64 uniquely exsit in that of donkeys, respectively. These insights enhance our understanding of the biological mechanisms underlying the reproductive distinctions between these equine species. Moreover, the identified species specific proteins may be essential for thier sperm quality and function, which holds practical value for breeding programs and investigations. Full article

Background: We utilized data-independent acquisition (DIA) to study the poorly understood biology of Mdm2 and MdmX in a p53-null context. Mdm2 and MdmX form an E3-ligase complex that has as its most well-studied function the negative regulation of the tumor suppressor p53; however, it is also known to interact with many other proteins in a p53-independent manner. Methods: In this work, small-molecule and siRNA-based technology were used to modify Mdm2/MdmX activity in a human non-small-cell lung carcinoma cell line lacking p53 expression. Study of the proteome of these cells helped identify biological processes where Mdm2 and MdmX may play roles in a p53-independent manner. Proteins from H1299 cells, treated with the drug MEL23 or siRNA against Mdm2 or MdmX, were analyzed. Results: Protein ontology and function were analyzed, revealing which pathways are affected by modulation of the proteins that form the complex. Insights into how those functions are dependent on the activity of the complex also gained via comparisons among the three groups of samples. Conclusions: We selected a potential target from the DIA analysis and validated it by immunoblotting and qPCR, and this allows us to demonstrate a new interaction partner of the Mdm2-MdmX complex in human cells. Full article

Background: Ammonia (NH₃), a harmful gas, reduces livestock productivity, threatens their health, and causes economic losses. Luteolin (Lut), an anti-inflammatory flavonoid, may counteract these effects. Methods: Our study explored luteolin’s protective mechanisms on chicken splenic lymphocytes under ammonia stress using a simulation model and four-dimensional fast data-independent acquisition (4D-FastDIA) proteomics. We identified 316 proteins, with 69 related to ammonia’s negative effects and 247 to Lut’s protection. Thirty differentially expressed proteins (DEPs) were common to both groups, with 27 showing counter-regulation with Lut. Results: Gene Ontology (GO) analysis showed DEPs enriched in molecular responses to interferons and the negative regulation of immune responses, mainly located extracellularly. Molecular function analysis revealed DEPs in antigen binding and synthase activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis linked DEPs to pathways like estrogen signaling, NOD-like receptor signaling, cytokine–cytokine receptor interaction, and JAK-STAT signaling. The quantitative real-time polymerase chain reaction (qRT-PCR) results indicated that the mRNA levels of Interferon Alpha and Beta Receptor subunit 2 (IFNAR2) and Signal Transducer and Activator of Transcription 1 (STAT1) were trending downward. This observation was in strong agreement with the downregulation noted in the proteomics analysis. Conclusions: Lut’s protective role against ammonia’s adverse effects on chicken splenic lymphocytes is linked to the modulation of key signaling pathways, offering insights for further research on treating ammonia exposure with Lut. Full article

To explore the differences in protein quality among classic medicinal entomopathogenic fungi and to evaluate their metabolic adaptability, we analyzed the amino acid composition and proteomic characteristics of Cordyceps sinensis (CS), Cordyceps militaris (CM), and Cordyceps cicadae (CC). Quantitative analysis showed CM contained the highest crude protein and lysine, methionine, threonine, and valine. CS adapted to high-altitude hypoxia and exhibited lower protein but elevated leucine, isoleucine, and histidine contents, which may contribute to membrane stabilization and oxidative stress resistance. CC displayed higher non-essential amino acids such as arginine, proline, and tyrosine, reflecting active nitrogen metabolism. Four-dimensional data-independent acquisition (4D-DIA) proteomics identified 495 differentially expressed proteins (DEPs). Compared with CS, CM and CC displayed upregulated glutamate oxaloacetate transaminases 2 (GOT2), glutamate dehydrogenase (GDH), and argininosuccinate synthase 1 (ASS1) coordinately regulate nitrogen flux through the alanine-aspartate-glutamate metabolic network and urea cycle, supporting metabolic intermediate replenishment for energy metabolism. The upregulation of branched-chain keto acid dehydrogenase E1 subunit alpha (BCKDHA) and acyl-CoA dehydrogenase short/branched chain (ACADSB) in CM and CC facilitated the integration of branched-chain amino acid catabolism with the TCA cycle, explaining species-specific differences in protein content. This study presents the first application of 4D-DIA proteomics to compare CS, CM, and CC, providing insights into quality divergence mechanisms in medicinal fungi. Full article

Haploid breeding technology has advantages in terms of saving time and reducing labor intensity and costs. However, the low induction rate limits the application of this technology. Previous researchers found that heat shock can increase the rate of Embryo-like structures (ELSs) induction. However, molecular mechanisms underlying heat-shocked haploid induction remain poorly understood. In the current study, unfertilized ovules of watermelon were subjected to heat shock for 0–5 days and conducted transcriptomics sequencing and DIA-based proteomics sequencing. Results indicated that, in contrast to the non-heat-shock condition, the expression level of protein phosphatase 2C (PP2C), a negative regulator in abscisic acid (ABA) signal transduction pathway, was repressed, and the expression level of Sucrose-non-fermenting 1-related protein kinases (SnRK2) was activated. The activated SnRK2s are enabled to promote the accumulation of storage substances in ovules. Through analysis, the expression of many genes involved in the biosynthesis of unsaturated fatty acids and amino acids has indeed been upregulated. In conclusion, our findings demonstrate that heat shock promotes the accumulation of storage substances in unfertilized ovules by activating the signal transduction process of ABA, which correspondingly increases ELSs induction rate. Full article

Identifying the specific factors secreted during early pregnancy is an effective method for pregnancy detection in cattle, helping to reduce empty pregnancies in the industry. To systematically investigate metabolic variations between early pregnancy and the estrous cycle and their relationship with pregnancy progression, this study utilized four-dimensional data-independent acquisition (4D-DIA) proteomics and liquid chromatography–tandem mass spectrometry (LC-MS/MS) metabolomics to analyze serum samples collected from Chinese native yellow cattle at day 0 and day 21 post-mating, combining bioinformatics analysis with experimental validation. The platelet activation signaling pathway and angiogenesis-related proteins were significantly upregulated. Among them, fibrinogen alpha/beta/gamma chains (FG) exhibited notable differences, with their branched-chain protein FGB showing highly significant upregulation (p = 0.003, Log₂FC = 2.167) and tending to increase gradually during early pregnancy, suggesting that FGB could be one of the important indicators of early pregnancy in Chinese native yellow cattle. Among the differential metabolites, 11-Deoxy prostaglandin F1α (p < 0.001, Log₂FC = 1.563), Thromboxane B1 (p = 0.002, Log₂FC = 3.335), and Homo-Gamma-Linolenic Acid (C20:3) (p = 0.018, Log₂FC = 1.781) were also increased, indicating their involvement in the regulation of the platelet activation signaling pathway. The platelet activation signaling pathway plays a crucial role in maternal immune tolerance and placental vascularization, which are essential for embryo implantation and placental development. These findings indicate that FGB has the potential to be a valuable biomarker for early cattle pregnancy detection, thereby improving pregnancy diagnosis accuracy, reducing economic losses caused by undetected empty pregnancies and enhancing reproductive efficiency in the cattle industry. Undoubtedly, our research outcomes must be validated with future studies, and a larger sample size as well as the evaluation of the potential endocrine effects induced by the synchronized estrus treatment must be considered. Full article

High-fat diets (HFDs) usually trigger disruptions in lipid metabolic processes and immune suppression in fish. As an eco-friendly and potent additive, the inclusion of probiotics in fish diets ameliorates dysregulations in lipid metabolism, mitigates oxidative stress, and reduces inflammatory reactions triggered by HFDs. However, little current research has focused on the improvement of the hazards of HFDs in fish by probiotics. Therefore, we employed 4-dimensional data-independent (4D-DIA) proteomic analysis to investigate the mechanism of the protective impact of probiotics against HFD-induced hepatic injury in Coilia nasus between the HFD group and the probiotic supplementation in HFD (PHFD) group. Additionally, lipid accumulation and antioxidant indicators in the liver were also measured via Oil Red O staining and activity detection. Administration of probiotics markedly attenuated the hepatic concentrations of triglycerides (TG), cholesterol (CHO), and low-density lipoprotein cholesterol (LDL-C) in C. nasus subjected to HFDs. Furthermore, it significantly upregulated the expression of the differentially expressed proteins (DEPs) implicated in cholesterol metabolism and fatty acid oxidation, while concurrently downregulating the DEPs associated with fatty acid synthesis. Additionally, probiotic supplementation significantly reduced the aspartate aminotransferase (AST), alanine aminotransferase (ALT), and malondialdehyde (MDA) levels induced by HFDs. It also upregulated the activities of catalase (CAT) and superoxide dismutase (SOD). Probiotic supplementation significantly upregulated the DEPs related to antioxidants, while significantly downregulating the DEPs associated with inflammatory responses and autophagy. These findings suggested that probiotics ameliorated HFD-induced hepatic lipid accumulation in C. nasus by enhancing cholesterol metabolism and fatty acid oxidation, concomitantly with the suppression of fatty acid synthesis pathways. Additionally, probiotics protected against HFD-induced hepatic injury by enhancing antioxidant defenses and suppressing inflammation in C. nasus. Full article

Cytokines are crucial in various physiological and pathological processes, especially in inflammatory diseases in mammals. However, the comprehensive identification of cytokines and their potential regulatory functions in the mammary glands of Holstein cows suffering from clinical mastitis (CM) remains only partially understood. This study aimed to systematically identify biological processes (BPs) and differentially expressed proteins (DEPs) associated with cytokines and to explore their functions through the analysis of previously obtained data from data-independent acquisition (DIA) proteomics. We confirmed that the dynamic balance between pro- and anti-inflammatory factors is closely associated with dairy mastitis. A total of 4 BPs, comprising 75 upregulated and 16 downregulated DEPs, were identified, particularly in relation to adiponectin (ADIPOQ), which strongly interacts with the other DEPs and participates in peroxisome proliferator-activated receptor (PPAR) and adipocytokine signaling pathways. Immunohistochemical and immunofluorescence staining revealed that ADIPOQ was predominantly localized in the cytoplasm of mammary epithelial cells. Moreover, the expression levels of ADIPOQ mRNA and protein in the mammary glands of the CM group were notably reduced compared to those in the healthy group. A potential mechanism of action of ADIPOQ was suggested, with findings indicating that a decrease in ADIPOQ expression could potentially worsen inflammation in CM. These results offer novel insights into cytokines and the regulatory mechanisms of ADIPOQ in Holstein cows with CM which may benefit the prevention and treatment of dairy mastitis. Full article