Search Results (1,253)

Background: Diabetes mellitus is characterized by chronic hyperglycemia, which promotes oxidative stress and endothelial dysfunction. MicroRNAs (miRNAs) have emerged as important regulators of diabetic vascular complications. Our previous RNA-sequencing study identified putative novel miR-1133 as an upregulated miRNA in hyperglycemia-induced human umbilical vein endothelial cells (HUVECs). This study aimed to investigate the potential involvement of putative novel miR-1133 in oxidative stress in hyperglycemia-induced HUVECs. Methods: Functional enrichment and protein–protein interaction (PPI) network analyses were performed to identify biologically relevant predicted target genes of putative novel miR-1133. Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) was selected for further investigation because it was identified as a hub gene in the PPI network and was involved in the enriched PI3K/Akt signaling pathway. HUVECs were exposed to high glucose (33.3 mM) to establish an in vitro hyperglycemic model, and the effects of transfection with putative novel miR-1133 inhibitor on PIK3CA expression and oxidative stress markers were evaluated. Results: Bioinformatic analyses identified PIK3CA as a hub gene among the predicted targets of putative novel miR-1133 and identified the PI3K/Akt signaling pathway as significantly enriched. Experimentally, hyperglycemia significantly reduced PIK3CA expression, whereas putative novel miR-1133 inhibitor transfection increased PIK3CA expression. Furthermore, putative novel miR-1133 inhibitor transfection was associated with reduced reactive oxygen species and 8-hydroxy-2′-deoxyguanosine levels, together with increased superoxide dismutase 1 (SOD1) mRNA expression and total SOD activity. Conclusions: Transfection with putative novel miR-1133 inhibitor was associated with increased PIK3CA expression and reduced oxidative stress markers in hyperglycemia-induced endothelial cells. Together, bioinformatic and experimental findings support an association between putative novel miR-1133 inhibitor transfection, PIK3CA expression, and oxidative stress under hyperglycemic conditions. Further studies are required to validate the direct interaction between putative novel miR-1133 and PIK3CA and to determine the relevance of these findings in vivo. Full article

Modulation of protein–protein interactions (PPIs) by small molecules is a vital strategy in drug discovery. Nevertheless, due to the inherent nature of PPI interfaces, practical implementation of this approach remains a high-hanging fruit in medicinal chemistry. In this report, we develop a new line of PEX14–PEX5 PPI inhibitors by homologation of a previously developed dibenzo[b,e]azepin-6(6H)-one scaffold. The challenging chemistry of 8-membered ring formation led to the development of novel PEX14 inhibitors featuring a 6+8+6 tricyclic system. The obtained analogs were tested for their capability of disrupting the PEX5-TbPEX14 PPI, as well as for in vitro activity against the T. brucei protist. Overall, the developed scaffold not only represents an interesting alternative for prospective trypanocidal TbPEX14 ligands but may also be useful in the design of inhibitors of other PPIs mediated by a similar topology of hydrophobic binding pockets. Full article

Network pharmacology has become a central paradigm in modern drug discovery, replacing the reductionist “one drug, one target” view with a systems-level understanding of how compounds engage networks of proteins that are linked to disease. Despite its impact, a typical network-pharmacology study remains fragmented and technically demanding: researchers must query several independent databases, install and reconcile multiple standalone tools for target collection, network construction, hub-gene ranking and pathway enrichment, and then manually bridge the results into structure-based follow-up such as molecular docking. This fragmentation is a persistent barrier, particularly for experimental and non-specialist users. Here, we present the network-pharmacology module of Drug Design Studio (DDS) 2.0, a unified, user-friendly platform that streamlines the entire workflow—disease target retrieval, compound–target prediction, shared-target identification, protein–protein interaction (PPI) network construction, hub-gene ranking and Gene Ontology/pathway enrichment—within a single guided interface, consolidating steps that otherwise require several separate tools. Crucially, DDS 2.0 links the resulting hub genes directly to the docking and virtual-screening engine introduced in the previous DDS releases: representative experimental structures and mutant forms—for instance, resistance-conferring variants found in drug-resistant strains—of the target proteins are selected and streamed into a docking-ready workspace, with dedicated support for covalent binders. We validate the module against four independent published network-pharmacology studies spanning diverse diseases; DDS reproduces the reported hub genes with a mean recovery (recall) of 0.85 (range 0.80–0.90) and a mean Jaccard index of 0.74, and recovers the corresponding target sets and enriched pathways. DDS 2.0 thus delivers an integrated route from systems-level analysis to structure-based drug design. DDS 2.0 is freely and publicly accessible. Comprehensive user documentation is built directly into DDS and can be accessed at any time from the Documentation panel. Full article

Background: Dystonia is a severe neurological disorder with enigmatic pathogenesis. Current treatment options are limited in preventing the disease progression, underscoring the urgent need for new targeted therapeutic agents to develop more effective therapies. Methods: We performed a proteome-wide Mendelian randomization (MR) study and sensitivity analyses to evaluate the causal relationships between dystonia and proteins. GO and KEGG enrichment analysis of dystonia-associated proteins was conducted. Then, we built PPI network and identified the expression of hub-genes in specific brain neurons in single-cell sequencing data. Additionally, we performed drug enrichment analysis of hub-genes, and employed network pharmacology and molecular docking methods to identify potential drugs for dystonia. Results: Our study identified genetically predicted associations consistent with a potential causal effect between 51 proteins and risk of dystonia. GO and KEGG enrichment analyses revealed that these proteins are involved cellular response to transforming growth factor-β stimulation and cytokine-cytokine receptor interaction. Notably, the PPI network exhibited 21 community relationships within the regulatory network among the 51 dystonia-associated proteins identified. The single-cell RNA annotations for brain cluster specificity revealed Tumor necrosis factor (TNF) was highly expressed in microglia cells. Drug enrichment analysis identified five traditional Chinese medicine monomers (paeoniflorin, artesunate, ginsenoside Rh1, psoralen, and quercetin dihydrate) as candidates for molecular docking analysis. Among these, paeoniflorin-TNF, quercetin dihydrate-TNF, and artesunate-TNF exhibited the highest binding energy (−9.1 kcal/mol). Conclusions: Our molecular-docking analysis suggested that traditional Chinese medicine monomers including paeoniflorin, quercetin dihydrate, and artesunate may serve as promising candidates for future drug development. Full article

Background/Objectives: Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with limited targeted therapeutic options. Although the anticancer and pro-apoptotic properties of boswellic acids have previously been reported, the interaction profile of chemically defined β-boswellic acid (BA) with doxorubicin (DOX) remains insufficiently characterised in the murine 4T1 TNBC-like model. This study quantitatively evaluated BA–DOX drug interactions using different reference models and characterised the cytotoxic and apoptosis-associated cellular phenotype accompanying combined exposure. Methods: Cytotoxicity was assessed using the MTT assay and BA–DOX interactions were evaluated using the Chou–Talalay combination index (CI), highest single-agent (HSA) and Bliss independence models. Apoptosis and cell-cycle distribution were analysed by flow cytometry and mitochondrial membrane potential was assessed by JC-1 staining. Caspase-3/7 activity, RT-qPCR, live/dead Calcein-AM/PI staining, 4′,6-Diamidino-2-phenylindole (DAPI) nuclear staining, and cytokine measurements were also performed. Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), and STRING-based protein–protein interaction (PPI) analyses were used to explore putative molecular pathways associated with experimental findings. Results: The 48 h selectivity index of BA was 1.28, indicating only modest differential cytotoxicity between 4T1 cells and HaCaT keratinocytes under the experimental conditions rather than definitive cancer-cell selectivity. Drug-interaction analyses revealed concentration- and model-dependent effects, with the Chou–Talalay analysis indicating synergism in selected intermediate and higher concentration pairs. Under the selected phenotypic-characterisation condition, BA + DOX produced a greater apoptotic response than either single treatment, accompanied by increased G2/M and Sub-G1 fractions, mitochondrial membrane depolarisation, and increased caspase-3/7 activity. This treatment condition was not included in the drug-interaction analysis and was therefore not interpreted as a pharmacologically validated synergistic combination. RT-qPCR demonstrated increased mRNA expression of Bax, Casp3, and Casp9, decreased mRNA expression of Bcl2, and a marked increase in the Bax/Bcl2 mRNA ratio. Calcein-AM/PI and DAPI analyses further demonstrated increased cell death and apoptotic nuclear alterations. The measured concentrations of TNF-α and IL-6 in culture supernatants were lower after BA + DOX treatment, whereas IL-10 remained unchanged; however, these cytokine measurements were not normalised to viable cell number and therefore require cautious interpretation. Exploratory bioinformatic analyses identified predicted associations with apoptosis-, mitochondrial-, and cell-cycle-related processes and pathways; however, these database-derived findings were considered hypothesis-generating and not evidence of BA-dependent target engagement or pathway activation. Conclusions: Combined BA and DOX exposure produced greater cytotoxic and apoptosis-associated responses than either single treatment in 4T1 cells, whereas formal drug-interaction classifications varied according to concentration and analytical model. The accompanying changes in mitochondrial membrane potential, caspase-3/7 activity, and apoptosis-related gene expression describe a treatment-associated cellular phenotype but do not identify a direct molecular target of BA or establish a causal molecular mechanism. The findings also do not demonstrate TNBC-specific selectivity. Further studies using additional breast cancer and tissue-matched non-malignant models, together with direct target-engagement and functional pathway-validation approaches, are required. Full article

Korean ginseng (Panax ginseng C. A. Meyer) is a perennial medicinal crop highly sensitive to waterlogging stress. Although excess soil moisture is known to induce oxygen limitation in the rhizosphere, the resulting metabolic constraints may precede visible shoot symptoms such as wilting, chlorosis, or necrosis. To examine the molecular responses under sustained high soil moisture before overt shoot necrosis, one-year-old ‘Yunpoong’ plants were exposed to ambient waterlogging at 45–55% volumetric soil water content (VSWC), while control plants were maintained at 25% VSWC. Phenotypic observations and hyperspectral imaging were conducted immediately after treatment initiation (week 0) and at weeks 1, 2, and 3, whereas whole-plant samples for RNA-seq were collected at weeks 1–3. Hyperspectral imaging and normalized difference vegetation index (NDVI) analysis indicated limited temporal changes in canopy-level spectral traits during the treatment period. In contrast, transcriptomic analyses revealed time-dependent changes in whole-plant gene expression. A total of 6448 unique differentially expressed genes (DEGs) were identified, of which 4369 were specific to week 3. Gene Ontology (GO) enrichment analysis suggested a stepwise adaptive pattern consisting of early priming, transient stabilization, and long-term remodeling. Hypoxia-, jasmonic acid-, and lignin-related processes were enriched at week 1, water deprivation and protein quality control responses were adjusted at week 2, and glycolysis, phosphate starvation, and repression of growth-related processes became prominent at week 3. Weighted gene co-expression network analysis (WGCNA) and STRING-based protein–protein interaction (PPI) analysis further identified functional modules associated with RNA processing, photosystem regulation, proteostasis, and central carbon, energy, and phosphate metabolism. Integrated transcriptome and network analyses prioritized six candidate genes, GAPC2, MDH, PGI1, PPC1, Lhb1B1, and RD21A, for further functional validation in relation to prolonged ambient waterlogging responses. Full article

Background and Objectives: Alzheimer’s disease (AD) is the most common neurodegenerative disorder, and current therapies provide only limited symptomatic relief without effectively slowing its progression. Increasing evidence suggests that aberrant activation of the Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling cascade contributes to AD-associated neuroinflammation. This study investigated the therapeutic potential and molecular mechanisms of JAK inhibitors in AD using integrated bioinformatics and network pharmacology approaches. Materials and Methods: Potential anti-AD targets of JAK inhibitors were identified using the SwissTargetPrediction and GeneCards databases. Functional enrichment, protein–protein interaction (PPI) analysis, transcriptomic validation using public datasets, regulatory network construction, molecular docking, normal mode analysis (NMA), and absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction were performed to investigate the potential mechanisms of action of these drugs in AD. Results: Our analysis identified 163 shared targets between JAK inhibitors and AD. Enrichment analysis revealed that these genes were primarily involved in protein phosphorylation and were enriched in key signaling pathways, including the neurotrophin, phosphoinositide 3-kinase/protein kinase B (PI3K/Akt), and mitogen-activated protein kinase (MAPK) signaling pathways. PPI analysis identified AKT1, BCL2, SRC, STAT3, and TNF as five highly ranked hub targets across multiple topological algorithms. Transcriptomic validation confirmed significantly higher expression of these targets in the prefrontal cortex of individuals with AD compared with normal subjects. Molecular docking indicated that pacritinib and momelotinib showed relatively favorable predicted interactions with the hub proteins, while NMA revealed differences in the predicted flexibility of the docked complexes. Furthermore, ADMET prediction showed that pacritinib possesses favorable pharmacokinetic properties for the treatment of AD. Conclusions: Collectively, these findings provide mechanistic insights into the potential effects of JAK inhibitors in AD and identify pacritinib as a computationally prioritized candidate that warrants experimental validation in appropriate AD models. However, as this study is based solely on computational analyses without wet-lab validation, the findings should be considered hypothesis-generating in silico evidence, and the potential safety concerns of pacritinib require further investigation. Full article

The decline in eggshell strength (ESS) during the late laying period is an important issue that needs to be addressed in the laying hen industry. Given that eggshell formation depends heavily on uterine mucosa secretions, understanding the underlying transcriptomic changes is essential. To investigate this, eggshell phenotypes were compared between the peak laying period (30 weeks of age, 30 W) and the late laying period (65 weeks of age, 65 W) of White Leghorn laying hens. Furthermore, RNA sequencing of the uterine mucosa was performed, and the sequencing data were quality-controlled, aligned to the chicken reference genome (GRCg7b), quantified using StringTie, and analysed for differential expression using DESeq2. WGCNA was subsequently performed to identify candidate genes associated with eggshell quality. The results showed that ESS decreased from 31.31 ± 3.34 N in the 30 W group to 24.65 ± 2.11 N in the 65 W group (p < 0.001). Transcriptomic analysis identified 903 differentially expressed genes (DEGs) in the uterine mucosa, and these DEGs were significantly enriched in pathways related to eggshell mineralisation. By integrating WGCNA, protein–protein interaction (PPI) network analysis, and trait correlation analysis, six candidate genes were identified: GNAS, BMPR2, EDN2, ANXA1, PLCB2, and CX3CL1. In conclusion, this study identifies new candidate genes and provides a theoretical basis for elucidating the molecular mechanisms underlying the decline in eggshell quality in late-laying hens. Full article

Chinese hickory (Carya cathayensis Sarg.) is an economically important tree species widely cultivated in southeastern China, where trunk canker disease caused by Botryosphaeria dothidea poses a serious threat to tree health and production. Pectin-degrading enzymes are important virulence-associated factors that facilitate fungal colonization and host tissue maceration, but their evolutionary diversification and functional roles in B. dothidea during woody host infection remain poorly understood. Comparative genomic analysis revealed lineage-specific variation in the GH28 glycoside hydrolase family among the examined Botryosphaeriaceae species, with B. dothidea exhibiting an expanded GH28 repertoire relative to the analyzed species. Expression analysis and functional assays revealed that BdGH28_3 showed the highest transcript abundance during infection stage and contributed to the full virulence of B. dothidea. A predicted protein–protein interaction (PPI) network suggested potential associations between BdGH28_3 and other pectinolytic enzymes, including polygalacturonases, pectin lyases, and pectinesterases. Collectively, these findings identify GH28 diversification as a distinctive feature of the B. dothidea genome and establish BdGH28_3 as a virulence-associated member, providing a foundation for investigating GH28-mediated pathogenicity in woody hosts. Full article

COVID-19 remains a relevant area of biomedical investigation because its pathogenesis involves complex virus–host interactions. This study aimed to explore, through purely in silico and hypothesis-generating insights, the predicted molecular associations between benzyl isothiocyanate (BITC) from Salvadora persica and COVID-19-associated host-response pathways. BITC-associated targets were collected from compound-target databases, while COVID-19-associated targets were obtained from disease-gene databases and transcriptomic datasets. Overlapping targets were analyzed using protein–protein interaction network construction, hub-gene prioritization, Gene Ontology and KEGG enrichment analyses, and molecular docking. A total of 271 unique BITC-associated targets and 1890 COVID-19-associated targets were identified, with 36 candidate targets overlapping. PPI analysis generated a connected network of 24 nodes and 39 edges. Hub-gene analysis prioritized ACE, JUN, MAOA, CDK1, MAOB, HCK, CCNA2, ACHE, GADD45A, and ADRA2A. Enrichment analysis indicated associations with inflammatory response, vascular regulation, calcium homeostasis, monoamine oxidase activity, NF-κB signaling, serotonergic synapse, and tryptophan metabolism. Validated active-site docking of six targets yielded comparative Vina scores ranging from −5.380 to −6.437 kcal/mol. These preliminary findings provide theoretical target–pathway associations supporting further investigation of BITC as a potential immunomodulatory candidate within COVID-19-related host-response pathways. Full article

Background/Objectives: Epoxide hydrolase 2 (EPHX2), which encodes soluble epoxide hydrolase (sEH), is involved in arachidonic acid metabolism and has been associated with inflammation, lipid metabolism, and tumor biology. However, its prognostic significance and biological associations in lung adenocarcinoma (LUAD) remain unclear. This study aimed to investigate the expression profile, prognostic value, and molecular pathways of EPHX2 in LUAD using bioinformatics analyses. Methods: EPHX2 expression was evaluated using TNMplot, GEPIA2, and GEO datasets, while protein expression was assessed using the Human Protein Atlas and CPTAC/UALCAN platforms. Prognostic analyses were performed using Kaplan–Meier Plotter, GEPIA2, and Human Protein Atlas datasets. Co-expression and gene set enrichment analyses were conducted using LinkedOmics, and functional enrichment analyses were performed using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome databases. Correlation and protein–protein interaction (PPI) analyses were evaluated using GEPIA2 and STRING. Results: EPHX2 expression was significantly reduced in LUAD tissues compared with normal lung tissues across datasets, and these findings were supported at the protein level. High EPHX2 expression was associated with better overall survival and retained independent prognostic significance in multivariate Cox analysis. Functional enrichment analyses demonstrated associations with lipid metabolism, arachidonic acid metabolism, cytochrome P450-related pathways, and oxidative processes. Correlation analyses suggested potential associations between EPHX2 and angiogenesis, extracellular matrix remodeling, and hypoxia-related pathways. Conclusions: Bioinformatics analyses suggest that EPHX2 may participate in metabolic and tumor progression-related regulatory networks and may serve as a prognostic biomarker in LUAD. Full article

Background/Objective: Cinnamaldehyde (CA) is a naturally occurring bioactive compound derived from the leaves, bark, roots, and flowers of the Chinese medicinal plant Cinnamomum cassia. It exhibits a broad spectrum of pharmacological properties, encompassing antioxidant, antibacterial, anti-diabetic, antifungal, and anticancer activities. Notably, it has shown potential therapeutic benefits in the management of type 2 diabetes mellitus (T2DM) and non-alcoholic fatty liver disease (NAFLD). Ochratoxin A (OTA), a common contaminant found in foods such as cereals, coffee, and raisins, is also present in traditional Chinese medicinal materials, including Astragalus and liquorice. T2DM and NAFLD share intertwined pathophysiological pathways, including insulin resistance, dyslipidaemia, chronic low-grade inflammation and oxidative stress, with insulin resistance serving as the common pathological hub for both conditions. Consequently, they frequently co-occur and exacerbate each other. OTA exerts dual-targeted toxicity to the pancreas and liver, which may synergistically drive the development of the comorbidity of T2DM and NAFLD. These two processes are mutually causal and together constitute the pathological basis of metabolic comorbidity. Methods: Network toxicology employs toxicological data, gene expression, and protein–protein interaction (PPI) networks to predict the targets of toxins, while network pharmacology, based on systems biology principles, reveals how drugs exert regulatory effects through multiple targets and pathways. In this study, we employed an integrated network toxicology and network pharmacology approach to jointly decipher the potential mechanisms by which CA intervenes in OTA-induced comorbid T2DM-NAFLD. First, a network toxicology approach was employed to preliminarily screen for core toxicological targets responsible for OTA’s pathogenicity. Subsequently, network pharmacology was used to identify potential targets of CA-mediated intervention in the disease. Finally, the common overlap among the CA intervention targets, OTA toxicity targets, and disease targets was defined as the final set of potential targets for CA-mediated intervention in OTA-induced T2DM-NAFLD comorbidity. A PPI network was constructed using the STRING database, and topological analysis was performed with Cytoscape. Core targets were selected using the median values of six parameters—betweenness centrality, closeness centrality, degree centrality, eigenvector centrality, LAC (local average connectivity) score, and network centrality—as cut-off thresholds, and the top 10 key genes were further identified using the cytoHubba plugin. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted via the DAVID database, and the results were visualized on the CNSknowall platform. Lastly, molecular docking of the core targets was performed using the CB-DOCK2 platform to validate binding affinity. Results: Based on an integrated analysis of network toxicology, network pharmacology, and molecular docking, 10 key targets were systematically identified. These may serve as potential mediators of cinnamaldehyde in the treatment of OTA-induced T2DM-NAFLD comorbidity. Among these, six targets—albumin (ALB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), interleukin-6 (IL-6), tumor necrosis factor (TNF), actin beta (ACTB), and estrogen receptor 1 (ESR1)—possess crystal structures amenable to molecular docking. KEGG enrichment analysis revealed that CA and OTA jointly participate in key pathological processes such as the cancer pathway, the lipid and atherosclerosis pathway, the advanced glycation end-products–receptor for advanced glycation end-products (AGE-RAGE) signaling pathway, the phosphatidylinositol 3-kinase–protein kinase B (PI3K-Akt) signaling pathway, the TNF signaling pathway, and the interleukin-17 (IL-17) signaling pathway. OTA exacerbates inflammatory responses, impairs insulin signaling, promotes hepatic steatosis, and disrupts systemic metabolic homeostasis, ultimately contributing to T2DM-NAFLD comorbidity. Conversely, cinnamaldehyde counteracts these pathological processes through multiple mechanisms, including antioxidant and anti-inflammatory effects as well as regulation of glucose and lipid metabolism, thereby restoring metabolic homeostasis. Conclusions: This study has preliminarily identified the toxicological targets of OTA and the potential intervention targets of CA, offering new avenues for preventing and intervening in OTA-induced metabolic toxicity. Furthermore, it provides a theoretical basis for CA as a potential multi-target therapeutic agent and presents novel insights worthy of further investigation into the prevention of T2DM-NAFLD comorbidity. Full article

Exploring protein–protein interaction (PPI) networks during cellular processes is critical for understanding the molecular mechanisms underlying these processes. PL (proximity labeling) is an emerging technique with the potential to be a powerful protein interactomics tool. It employs proximity-labeling enzymes, coupled with mass spectrometry, to covalently label, capture, and identify interacting and neighboring proteins of the bait protein. The development of numerous novel PL enzymes and the improvement of biotin ligase-based enzymes have enabled efficient spatiotemporal mapping of PPIs, especially after the establishment of TurboID in plants. Most PL-associated reviews in plants focus on the potential applications of different enzyme-based PL. Here, we focus on PL cases effectively applied in plants and dissect each case in detail from the perspectives of PL expression design, labeling, extraction, enrichment, and quantitative proteomic identification. Moreover, we compare cases using biotin ligase-based PL (such as BioID and TurboID) and PUP-IT, highlighting the advantages and limitations of each PL system. We delineated the pipeline and optimization strategies for PL experiment design to facilitate successful execution by plant researchers. Full article

Tuberculosis (TB), caused by the intracellular pathogen Mycobacterium tuberculosis (Mtb), remains a major global health challenge. The prolonged duration of treatment and the emergence of multidrug-resistant strains have highlighted the need for alternative therapeutic strategies. This study investigated the therapeutic potential of Ag85A aptamer-conjugated PEGylated niosomes encapsulating ethanolic extract of propolis (Ag85A-PEGNio/EEP) using Mtb-infected macrophage model. Ag85A-PEGNio/EEP exhibited efficient cellular uptake, with more than 99.8% internalization by macrophages, and trafficked host phagolysosome, facilitating targeted delivery of EEP to intracellular Mtb. Ag85A-PEGNio/EEP treatment showed an anti-mycobacterium efficacy by reducing intracellular Mtb viability by approximately 51.2% compared with untreated controls. Moreover, Ag85A-PEGNio/EEP modulated macrophage immune responses by significantly increasing the expression of the pro-inflammatory cytokines IL-12 (8.4-fold) and IL-6 (3.8-fold), while markedly decreasing the expression of the anti-inflammatory cytokine IL-10 (6.4-fold). Protein–protein interaction (PPI) network analysis further revealed the association of proteins with immune regulation and antioxidant responses in treated cells. These findings suggest that Ag85A-PEGNio/EEP functions as a dual-action therapeutic platform by enhancing intracellular anti-mycobacterial activity while balancing host immune responses. This targeted nano-delivery system represents a promising candidate for host-directed TB therapy and further investigations are needed to validate these outcomes and explore their potential applications against TB treatment challenges. Full article

Background: Osteoarthritis (OA) is a prevalent degenerative joint disease with a complex molecular basis. This study aims to identify key molecules involved in OA pathogenesis, focusing on the role of acetylation-related gene expression. Methods: Public microarray datasets GSE82107 and GSE169077 were integrated to construct a differential expression landscape between OA patients and healthy controls. Acetylation-linked differentially expressed genes (acetylation-DEGs, ARDEGs) were extracted by intersecting DEGs with a curated set of acetyltransferases, deacetylases and acetylation substrates. A protein–protein interaction (PPI) network was built and subjected to LASSO-penalized regression to prioritise hub genes. Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Set Variation Analysis (GSVA) were performed to characterize biological themes. Immune infiltration was quantified with CIBERSORTx and single-sample Gene Set Enrichment Analysis (ssGSEA). Single-cell RNA-seq data (GSE216651) were employed for orthogonal validation. For experimental corroboration, synovial tissue was collected from OA patients undergoing arthroplasty; mRNA and protein levels of hub genes were determined by qRT-PCR, Western blot and immunofluorescence. The destabilisation of the medial meniscus (DMM) mouse model was used for in vivo verification. Results: Twenty-one high-confidence ARDEGs were identified. Analysis of the PPI network yielded ten hub nodes, six of which (EGR1, PFKFB3, HDAC4, MMP13, PDK4 and ACADL) retained non-zero coefficients in the least absolute shrinkage and selection operator (LASSO) model. Enrichment analyses implicated these genes in embryonic development, collagen-containing extracellular matrix remodeling and PI3K–Akt signaling. Immune infiltration analysis showed potential differences in immune cell abundance between OA and healthy controls. Single-cell dataset analysis verified the expression patterns of key genes in different cell types. Concordant dysregulation of EGR1, PFKFB3, HDAC4, MMP13 and PDK4 was observed at both mRNA and protein levels in human OA synovium and DMM mouse joints. Conclusion: This comprehensive analysis identified acetylation-related genes and analyzed their potential biological roles in OA. The identified ARDEGs may provide new insights into OA diagnosis and treatment. Full article