Search Results (1,191)

Methyl methacrylate (MMA)-based materials are widely used in temporary and permanent prosthetic dentistry; the prolonged presence of these materials in the oral cavity and potential residual monomer release can affect local biological responses. This study aimed to evaluate the biocompatibility and toxicity profiles of MMA, the monomeric unit of polymethyl methacrylate (PMMA), a key component of dental materials used in temporary prosthetic restorations. Molecular docking simulations were performed using CB-Dock2 and Autodock vina, while protein–protein interaction (PPI) analysis was performed using STRING and Cytoscape. In addition, Swiss ADME Target Prediction, toxicity prediction, and enrichment analyses were used to characterize the biological significance of selected targets in more detail. Molecular docking studies revealed promising interactions of MMA with valuable biomolecular targets relevant to biocompatibility. The toxicity profile revealed aspects of MMA that could be improved. Pharmacophore modeling, highlighting the importance of carbonyl and hydroxyl groups as pharmacophoric properties, revealed compounds with suitable biocompatibility profiles. Consequently, it emphasizes the interactions of MMA with biomolecules and safety considerations. It can guide the design and optimization of biocompatible materials as an exploratory avenue for future developments in dental biomaterials. Full article

Disease comorbidity—the co-occurrence of two or more diseases in the same individual—has gained growing attention due to its association with adverse clinical outcomes and increased treatment complexity. Recent subgraph-based approaches for disease comorbidity prediction model disease modules as subgraphs induced by disease-associated genes in the protein–protein interaction (PPI) network and learn disease representations from subgraph topology. However, these approaches are constrained by incomplete disease–gene annotations, which may obscure important molecular relationships between diseases. Accordingly, disease comorbidity may also be influenced by molecular events beyond annotated disease genes, such as gene fusion events that have emerged as important contributors to disease mechanisms. Motivated by the role of gene fusions in disease development, we introduce Gene Fusion-Initiated Path Propagation for Disease Comorbidity Prediction (FuDiCo), a framework that models comorbidity through influence propagation over the PPI network. FuDiCo represents fusion-associated genes as localized perturbation sources and learns how their influence propagates along interaction paths toward disease subgraphs, thereby capturing propagation patterns that link related diseases and contribute to their comorbidity. Experiments on a benchmark disease comorbidity dataset show that FuDiCo outperforms state-of-the-art methods, achieving statistically significant improvements. These results shed light on the importance of gene fusion events in understanding disease relationships. Full article

Objectives: This study aimed to identify core genes associated with mitochondria-related transcriptomic signatures and evaluate their potential as computational biomarkers, immune characteristics, regulatory mechanisms, and potential therapeutic relevance. Methods: Obesity-related transcriptome datasets were obtained from the GEO database. Differentially expressed genes (DEGs) were intersected with mitochondria-related genes (MRGs) to identify obesity-related MRGs. Functional enrichment, protein–protein interaction (PPI) analysis, CytoHubba, LASSO and random forest algorithms were used to screen core genes. External validation, ROC analysis, immune infiltration analysis, regulatory network construction, candidate drug prediction, and molecular docking were further performed. Results: A total of 527 DEGs and 15 differentially expressed MRGs were identified. Enrichment analysis suggested that these mitochondria-related genes were mainly associated with disrupted mitochondrial energy metabolism, lipid metabolic remodeling, and altered substrate utilization. ECHDC2, FASN, NAT8L, and AASS were identified as core MRGs; these genes are respectively associated with mitochondrial metabolic regulation, de novo fatty acid synthesis, N-acetylaspartate-related mitochondrial metabolism, and lysine degradation. These genes were significantly downregulated in obesity and showed good diagnostic performance. Immune infiltration analysis revealed alterations in the immune microenvironment, and the core genes were negatively correlated with multiple immune cell types. Molecular docking showed that Genistein had the lowest predicted binding free energy with NAT8L (−8.89 kcal/mol), suggesting relatively favorable binding among the tested ligand–target pairs. Conclusions: ECHDC2, FASN, NAT8L, and AASS may serve as candidate computational biomarkers, among which FASN represents a known lipid metabolism-related gene, supporting the biological plausibility of the workflow. Full article

Pinus massoniana Lamb. is an important native economic and ecological tree species in southern China. However, adventitious root regeneration severely restricts the asexual propagation of elite traits. The WOX gene family, a plant-specific transcription factor family, plays critical roles in various aspects of plant growth and development, particularly in root development, including the maintenance of the root apical meristem, root elongation, and the initiation and formation of lateral roots. In this study, a total of 21 WOX family proteins were identified from the genome of P. massoniana and designated as PmWOX1 to PmWOX21 based on their chromosomal locations. These 21 members were unevenly distributed across nine chromosomes, with a clustered distribution observed on chr7. Collinearity analysis suggested that gene duplication and purifying selection may serve as key driving forces in the evolution of WOX genes. Conserved motif analysis revealed divergence among different PmWOX clades, implying distinct functions in growth and development. Cis-element analysis indicated that PmWOX genes may be involved in the regulation of stress responses, hormone signaling, and developmental processes. Expression pattern analysis based on transcriptome data from root tips and shoot tips identified nine PmWOX genes with significantly higher expression in root tips. RT-qPCR further screened PmWOX4, which exhibited the highest expression in root primordia. Functional experiments verified that PmWOX4 genes encoded nuclear-localized proteins with transcriptional activity. The PPI results indicate that PmWOX4 may interact with CLE41/44, LBD, ATHB8 and CLV3/CLV1 to regulate adventitious root formation. Collectively, our findings suggest that PmWOX4 possesses functional potential in adventitious rooting, which could be further exploited to improve the efficiency of asexual propagation in P. massoniana. Full article

Epithelial ovarian cancer (EOC) remains one of the most aggressive gynecological malignancies, largely due to late-stage diagnosis, therapeutic resistance, and molecular heterogeneity. This study aimed to identify biologically relevant hub genes and evaluate potential dual-target compounds against Cyclin-Dependent Kinase 1 (CDK1) and DNA Topoisomerase II Alpha (TOP2A) through an integrated computational framework. Transcriptomic datasets from GSE28799, GSE54388, and GSE14407 were analyzed to identify overlapping differentially expressed genes, followed by protein–protein interaction analysis, functional enrichment, survival assessment, molecular docking, ADMET profiling, and molecular dynamics simulations. Mechanistically, CDK1 and TOP2A participate in coordinated cell-cycle regulation associated with G2/M progression and chromosomal dynamics in ovarian cancer. Among the identified hub genes, CDK1 and TOP2A demonstrated marked overexpression and central topological importance within the interaction network. Functional enrichment analyses highlighted significant associations with mitotic cell-cycle regulation, DNA replication, and proliferative signaling pathways. Molecular docking analyses identified Naringin as a potential dual-target candidate with favorable binding affinity toward both CDK1 and TOP2A. ADMET profiling suggested acceptable pharmacokinetic and toxicity characteristics, while molecular dynamics simulations supported stable protein–ligand interactions under dynamic conditions. Although survival analyses did not demonstrate statistically significant independent prognostic associations, the findings support the biological relevance of CDK1 and TOP2A in EOC progression. Collectively, this study provides an integrated computational perspective on CDK1/TOP2A-associated oncogenic signaling and prioritizes Naringin as a preliminary candidate for future experimental investigation in epithelial ovarian cancer. Full article

Protein–protein interactions (PPIs) represent one of the major factors determining structure, function and quality in food products, especially in the case of industrial processing. Within complex food matrices, the structural and physical behavior of food components is controlled by PPIs that determine aggregation behavior, network formation, phase stability, and structural integrity and are thus directly related to the stability of the final product and how well a product may perform during a process. Recent developments in analytical techniques have facilitated the elucidation of PPIs and their application in activity-induced structural changes, in particular during thermal, non-thermal, enzymatic, and mechanical processes. In lieu of providing an exhaustive summary, this review synthesizes research evidence and findings related to measuring PPIs from main food systems, namely dairy, meat, cereal and plant-based products. The impact of different processing methods on PPIs and related quality characteristics including structure, stability and functional activity is critically assessed. Knowledge gaps and methodological limitations (in particular concerning laboratory scale industrial processes) are highlighted. By combining mechanistic considerations with practical performance considerations, this review allows us to rationalize the improvement of food processing strategies and to develop protein-based foods with better quality and performance stability. Full article

Objectives: To investigate the potential mechanisms of maternal pregestational diabetes-induced neural tube defects (NTDs) by integrating proteomic data and histone H4 lysine 5 acetylation (H4K5ac) ChIP-seq data from the mouse model. Methods: The diabetic mouse model was established by intraperitoneal injection of streptozotocin (STZ) into female friend leukemia virus B strain (FVB) mice, with subsequent blood glucose monitoring. Diabetic females were then mated with healthy males, and embryonic tissues were collected on embryonic day 9.5. Among the embryos obtained from diabetic pregnancies, six NTDs embryos and six control embryos were selected for protein expression profiling using tandem mass tag (TMT)-labeled liquid chromatography-tandem mass spectrometry (LC-MS/MS), as well as for assessment of H4K5ac modification by ChIP-seq. Multi-omics integration was performed to identify common differentially expressed genes, followed by functional enrichment analysis. Key genes were validated using RT-qPCR. Results: Proteomic analysis revealed that differentially expressed proteins were significantly enriched in focal adhesion pathway. Protein–protein interaction (PPI) network analysis indicated that these proteins (e.g., Integrin alpha 3 (Itga3), glycogen synthase kinase 3 beta (Gsk3b), mitogen-activated protein kinase 9 (Mapk9)) were associated with focal adhesion and cytoskeletal functions. Integrated multi-omics analysis identified 923 common differentially expressed genes, which were also significantly enriched in focal adhesion pathway. Within this pathway, the protein expression levels of Itga3, Gsk3b, and Mapk9 exhibited a consistent co-variation trend with H4K5ac enrichment. RT-qPCR results confirmed that Itga3 was significantly up-regulated, while Gsk3b was down-regulated in the NTDs group (p < 0.05). Conclusions: Maternal pregestational diabetes may contribute to NTDs by disrupting cytoskeletal reorganization, cell adhesion, and migration processes. This disruption is likely mediated through H4K5ac-regulated expression of key focal adhesion pathway genes such as Itga3 and Gsk3b. Full article

Background: Esophageal squamous cell carcinoma (ESCA) represents one of the most common aggressive malignancies worldwide. Insulin-like growth factor binding protein 1 (IGFBP1), a typical member of the IGF superfamily, is closely linked to adverse prognosis in numerous cancers. Up to now, little is known about its functional relevance to cell migration and tumor progression in ESCA. This work focuses on clarifying the relationship between IGFBP1 expression and the progression and migratory characteristics of ESCA. Methods: mRNA expression profiles from ESCA patients were obtained from the TCGA and GEO databases. Differential expression analysis was performed using R software(version 4.2.2), followed by an intersection of DEGs between datasets. The STRING database was applied to establish PPI networks. Cytoscape software(Version 3.7.2) was then used for visual presentation and hub gene identification. IGFBP1 expression was validated in ESCA tissues versus adjacent normal tissues. Prognostic correlation was assessed using GEPIA, while diagnostic and predictive values were evaluated through ROC analysis and Cox regression. Genetic alterations of IGFBP1 were analyzed via cBioPortal. Immune cell infiltration patterns were investigated using TIMER. Functional enrichment analyses (GO, KEGG) were performed on IGFBP1-associated DEGs. In the in vitro experiments, esophageal cancer cell lines (such as Eca109 and TE-1) and normal human esophageal epithelial cell lines (such as HEEC) were selected. The transcriptional level of IGFBP1 was examined using RT-qPCR, while Western blot analysis was conducted to validate its protein expression changes. Changes in the proliferative capacity of cancer cells after IGFBP1 silencing were detected by the CCK-8 assay, and cell migration capacity was determined via wound scratch assays to clarify the related biological effects. Results: Overall, 2870 DEGs were screened from the GEO database, 153 DEGs were screened from the TCGA database, and 34 genes were found to be common to both databases; 10 core genes were screened from the PPI network. IGFBP1 was abnormally expressed in esophageal cancer. Cox regression confirmed that IGFBP1 is an independent risk factor, and prognostic analysis indicated that IGFBP1 is closely associated with poor prognosis. Gene mutation analysis showed that amplification mutations are the most common type of IGFBP1 gene mutation, and genetic alterations in IGFBP1 in ESCA patients are significantly associated with overall survival (OS) (p = 0.0002568). GO analysis indicated that IGFBP1-related differentially expressed genes were enriched in organic anion transport, epidermal development, apical cell components, and metal ion transmembrane transporter activity. Pathway enrichment based on the KEGG database illustrated the main enrichment of target genes in neuroactive ligand–receptor interactions, calcium signaling and cAMP signaling pathways. Additionally, remarkable differences in immune cell infiltration were observed between IGFBP1 high-expression and low-expression subgroups through tumor immune profiling. IGFBP1 expression differed significantly between esophageal cancer cells and normal esophageal epithelial cells, as detected by RT-qPCR (p < 0.05). Moreover, knockdown of IGFBP1 markedly inhibited the proliferation (p < 0.05) and migration abilities (p < 0.05) of TE-1 and Eca109 cells. Conversely, IGFBP1 overexpression facilitated these cellular processes. Conclusions: As a key oncogenic driver for ESCA, IGFBP1 may participate in the oncogenesis of ESCA, possibly influencing clinical outcomes via IGF signaling and the tumor microenvironment. Its dual functions in tumor and immune systems suggest it might be a candidate for ESCA immunotherapy research. Full article

Hantaviruses are emerging zoonotic pathogens responsible for two severe clinical syndromes: (i) haemorrhagic fever with renal syndrome (HFRS) and (ii) hantavirus cardiopulmonary syndrome (HCPS), collectively causing more than 200,000 human cases annually worldwide. Despite their public-health importance, the molecular mechanisms governing the host response and the population-level dynamics of rodent-to-human spillover remain incompletely characterised. The timeliness of this framework is underscored by the April–May 2026 outbreak of Andes orthohantavirus aboard the MV Hondius cruise ship, the first such cluster in a maritime setting, with three deaths reported across multiple countries. This event revealed critical gaps in existing models that treat humans solely as dead-end spillover hosts. Our coupled Susceptible-Exposed-Infectious-Recovered-Dead (SEIRD) model assumes no human-to-human transmission and is therefore designed for hantavirus strains where spillover does not lead to secondary human cases, specifically Hantaan virus (HTNV), Puumala virus (PUUV), Sin Nombre virus (SNV), and Dobrava-Belgrade virus (DOBV). The Andes virus (ANDV) outbreak aboard the MV Hondius is used as a real-world case study to assess the boundaries of our model and to motivate future extensions, not as a direct validation target for its quantitative predictions. Here, we present an integrated computational study combining three complementary analyses. First, we performed a preliminary phylogenetic analysis of the viral sequence, identifying Orthohantavirus andesense as the likely etiological agent responsible for the vessel-associated outbreak. Second, we carried out a downstream transcriptomic analysis of Hantaan virus (HTNV)-infected human umbilical vein endothelial cells (HUVECs), using publicly available RNA-seq data (GEO accession GSE133751, $n=3$ per group). This analysis identified 184 upregulated and 19 downregulated genes, highlighting a transcriptional response dominated by interferon-stimulated genes (ISGs), including CXCL10, CXCL11, MX2, DDX58, IRF7, STAT1, OASL, and CMPK2. We then constructed a protein–protein interaction (PPI) network using STRING, comprising 176 nodes and 3210 edges, and applied a composite network centrality score to rank putative regulatory hubs. This analysis identified ISG15, IRF1, CXCL10, STAT1, and DDX58 as the most central nodes. Pathway enrichment analysis confirmed a strong activation of interferon signalling (Reactome, $p=1.3\times {10}^{-63}$), antiviral defence mechanisms (Gene Ontology, $p=3.8\times {10}^{-58}$), and NF-$\kappa$B-related pathways, together with a concurrent suppression of ribosomal translation. Finally, we developed a coupled SEIRD epidemiological model that explicitly represents rodent-to-rodent and rodent-to-human transmission with logistic rodent population growth. Preliminary simulation analysis demonstrates that reducing human exposure to rodent excreta is substantially more effective than rodent population control alone for reducing human disease burden, and that rodent control in isolation can paradoxically increase human cases through a dilution-like effect. The integrated framework provides molecular and epidemiological insights relevant to hantavirus surveillance, therapeutic target identification, and public-health intervention design. Full article

Objective: To elucidate the role of cytoskeleton-associated protein 2 (CKAP2) in gastric cancer (GC) progression and evaluate its prognostic and potential protective significance. Methods: The candidate genes for GC were identified using differential expression and weighted gene co-expression network analysis (WGCNA). A panel of machine learning algorithms was applied for obtaining the key genes and yielding the hub target gene CKAP2 through protein–protein interaction (PPI) networks and single-cell RNA sequencing analysis. Further, the functional role of CKAP2 was explored through single-cell virtual knockout and pathway enrichment analysis. Meanwhile, the survival analysis and Mendelian randomization (MR) were used to evaluate the clinical relevance and causality of CKAP2. Finally, the expression of CKAP2 was further validated in clinical tissues and GC cell lines through Western blot. Results: A total of 20 candidate genes were identified, of which 8 were identified as hub genes through machine learning. Integrative PPI and single-cell analyses ultimately identified CKAP2 as the key gene. Virtual knockout analysis showed that the related differentially expressed genes were significantly enriched in the 5-HT pathway. Survival analysis demonstrated that elevated CKAP2 expression was associated with improved prognosis. MR analysis further suggested that CKAP2 might act as a protective factor, while 5-HT was associated with an increased risk of GC. Experimental validation confirmed that CKAP2 is significantly upregulated in GC tissues and cell lines. Conclusions: CKAP2 is a potential prognostic biomarker and protective factor in GC, possibly exerting its effects through regulation of the 5-HT pathway. These findings provide new insights into the mechanisms and potential therapeutic targets of GC. Full article

The PIN-LIKES (PILS) gene family is crucial for regulating auxin homeostasis and stress adaptation in plants; nevertheless, a comprehensive study on this family in alfalfa (Medicago sativa) remains insufficient. This research found 46 MsPILS genes within the tetraploid alfalfa genome and categorized them into four subfamilies. The genes are irregularly allocated throughout 16 chromosomes, with tandem duplications acting as a primary catalyst for family expansion. Analysis indicated that all MsPILS proteins contain the conserved Mem_trans domain. The promoter study revealed that MsPILS genes had many cis-elements that respond to abiotic stressors and hormones. qRT-PCR research indicated that MsPILS genes exhibit variable expression across several tissues and respond to multiple abiotic stressors. Protein–protein interaction (PPI) research revealed PIN3, PIN5, and PIN6 as principal interacting partners of the MsPILS proteins. Subcellular localization studies indicated that MsPILS1c is in the nucleus, plasma membrane, and endoplasmic reticulum (ER). This research offers significant genetic resources and a theoretical framework for elucidating the activities of PILS genes and for molecular breeding aimed at improving stress tolerance in alfalfa. Full article

Background: Polyamide 6 microplastics (PA6-MPs), as emerging environmental pollutants, have attracted increasing attention due to their potential health risks. Their accumulation in human intervertebral disc tissue (86.4 particles/g) suggests a possible role in intervertebral disc degeneration (IVDD). However, direct evidence and mechanistic understanding remain limited. This study aimed to investigate the association between PA6-MPs exposure and IVDD, based on the hypothesis that PA6-MPs promote IVDD progression by targeting key regulatory molecules and disrupting cellular homeostasis. Methods: Potential PA6-related targets were predicted using multiple public databases, and IVDD-related differentially expressed genes were obtained from the GEO database. Overlapping targets were identified and analyzed through protein–protein interaction (PPI) network construction, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to screen core targets and pathways. Molecular docking was performed to evaluate PA6–protein binding. In vitro validation was conducted using primary human nucleus pulposus cells exposed to PA6-MPs, with cell viability, proliferation, and phenotypic changes assessed by CCK-8, EdU, live/dead staining, and immunofluorescence (IF). Results: A total of 222 PA6-related targets and 1035 IVDD-associated genes were identified, yielding 10 overlapping targets. Four core targets, including NR3C1 and HDAC1, were selected. Molecular docking and experiments demonstrated stable binding and concentration-dependent inhibition of cell viability and proliferation. Conclusion: PA6-MPs may accelerate IVDD progression in a concentration-dependent manner by targeting key molecules and perturbing inflammatory homeostasis. These findings link environmental exposure to IVDD and provide a basis for future risk assessment and targeted intervention strategies. Full article

Pulmonary arterial hypertension (PAH) is a fatal vascular disorder with poor prognosis. 6:2 chloro-polyfluorooctane ether sulfonate (F-53B), a persistent environmental contaminant detected in humans, is known to be vasculotoxic, yet its association with PAH remains unexplored. This study aims to elucidate the mechanisms linking F-53B exposure to PAH by integrating network toxicology, molecular docking and in vitro experiments. Potential F-53B targets were predicted using ChEMBL, PharmMapper, and TargetNet. PAH-related genes were compiled from GeneCards, Online Mendelian Inheritance in Man (OMIM), Therapeutic Target Database (TTD), and GSE254617. We identified 42 key targets of F-53B-related PAH. Functional enrichment revealed terms such as inflammatory response and extracellular matrix. Protein–protein interaction (PPI) analysis identified five hub genes: CCL2, CXCL8, CCL5, CCR2, and CCL11. Molecular docking confirmed strong binding between F-53B and these core targets, with CCR2 showing the strongest affinity (−10 kcal/mol). Molecular dynamics simulations further verified stable binding to CCR2. In vitro experiments demonstrated that F-53B activated the CCL2/CCR2 axis and induced IL-1β, TNF-α, and IL-6 in HUVECs and RAW264.7 cells. This study reveals that F-53B is linked to PAH through dysregulation of chemokine signaling networks and induction of inflammatory cytokines. These findings suggest F-53B as a potential environmental risk factor for PAH and pinpoint potential targets for intervention. Full article

Myocardial fibrosis is a common pathological feature of multiple cardiovascular diseases, including heart failure, hypertension, and myocardial infarction, and is associated with poor prognosis. Despite extensive research, clinically validated molecular biomarkers for early diagnosis and reliable therapeutic targets for myocardial fibrosis remain limited. Post-translational modifications (PTMs), including phosphorylation, acetylation, ubiquitination, SUMOylation, and glycosylation, are critical regulators of fibrosis-related signaling pathways, yet a systematic bioinformatics-driven identification of PTM-related hub genes has not been performed. Three publicly available GEO datasets (GSE57345, GSE133054, GSE76314) comprising cardiac tissue from heart failure and control patients were integrated. Differentially expressed genes (DEGs) were identified using the limma package, then intersected with a curated PTM gene set derived from PhosphoSitePlus and UniProt databases. Weighted gene co-expression network analysis (WGCNA) identified fibrosis-associated modules, and protein–protein interaction (PPI) network analysis via STRING and CytoHubba pinpointed hub genes. Diagnostic performance was assessed by receiver operating characteristic (ROC) analysis across independent validation cohorts. Immune cell infiltration was estimated using CIBERSORT.Molecular docking with AutoDock Vina (version 1.2.3) was performed to evaluate binding affinity of FDA-approved cardiovascular drugs against identified hub protein targets. A total of 863 DEGs were identified in the training cohort (|log₂FC| > 1.0, adjusted p < 0.05), of which 138 overlapped with the PTM gene set. WGCNA revealed a turquoise module (r = 0.79, p < 0.001) most significantly correlated with fibrosis severity. PPI analysis identified five hub genes: SIRT3, SMAD3, NEDD4L, UBC9, and CAMK2D. ROC analysis demonstrated strong diagnostic performance (AUC range: 0.82–0.92) validated in independent cohorts. Hub genes showed significant correlations with M2 macrophage infiltration. Molecular docking identified spironolactone and finerenone as top-ranked ligands with binding energies of −8.7 and −8.4 kcal/mol against SMAD3 and SIRT3, respectively. This study, which is entirely in silico and based on publicly available transcriptomic datasets, systematically identifies five PTM-related hub genes as candidate diagnostic biomarkers and prioritised drug-repurposing targets in myocardial fibrosis. These findings are hypothesis-generating and require experimental validation (protein-level confirmation, cell- and animal-based functional assays, and biophysical binding studies) before any diagnostic or therapeutic claim can be made. Full article

Coffee consumption has been associated with metabolic and cardiovascular health, but the molecular mechanisms underlying these associations remain unclear. This study investigated the association between coffee intake and circulating proteomic profiles across metabolic conditions using a pooled-serum, exploratory design. Participants were classified into four groups: normal weight (NW), normal weight with coffee intake (NWC), obese with hypertension (OBHT), and obese with hypertension with coffee intake (OBHTC). Differentially expressed proteins (DEPs) were identified using volcano plot criteria (|log₂FC| ≥ 1, FDR < 0.05), followed by Reactome pathway enrichment, Gene Ontology (GO) molecular function, and Enrichr-derived protein–protein interaction (PPI) analyses. Results: In NW vs. NWC, coffee intake was associated with proteins enriched in receptor-mediated signaling and phosphoinositide pathways. In OBHT vs. OBHTC, DEPs were linked to mitochondrial respiration and oxidoreductase activity. The NW vs. OBHT comparison showed downregulation of metabolic and signaling proteins with enrichment of mitochondrial and stress-response functions. In NWC vs. OBHTC, proteins related to cytokine signaling and vascular function were reduced, while redox-associated regulators were increased. PPI networks highlighted interconnected hubs integrating signaling, metabolism, and immune responses. Conclusion: These findings suggest context-dependent proteomic patterns associated with coffee intake. Given the pooled design and small sample size, results are hypothesis-generating and require validation. Full article