International Immunopharmacology

Triggering receptor expressed on myeloid cells 2 (TREM2) plays a crucial role in regulating various microglial functions, including phagocytosis, inflammation, chemotaxis, and proliferation. Recent studies have demonstrated that TREM2 cooperates with DAP12 to mediate intracellular signaling essential for these processes. Despite the importance of the TREM2-DAP12 complex in microglial physiology, the mechanisms controlling its expression and activity remain poorly understood. In this study, we report that the soluble ectodomain of TREM2 (sTREM2) regulates microglial phagocytic activity by attenuating the surface expression of DAP12. We found that stimulation of the microglial cell line BV2 with recombinant sTREM2 reduces the membrane expression of DAP12, but not that of TREM2. In addition, sTREM2 binds to full-length TREM2, leading to the uncoupling of TREM2 from DAP12. Furthermore, pre-treatment of BV2 cells with sTREM2 significantly inhibited amyloid-{beta} incorporation. These findings suggest that sTREM2 negatively regulates TREM2 signaling through the destabilization of the TREM2-DAP12 complex, and act as a novel bioactive molecule that modulates TREM2 signaling under physiological and pathological conditions.

The activation of thermogenesis in brown adipose tissue (BAT) represents a pivotal target for ameliorating disorders of glucose and lipid metabolism. This study sought to elucidate the regulatory effects of quercetin on thermogenesis and glucose-lipid metabolism within brown adipocytes, alongside its underlying molecular mechanisms. The findings demonstrated that quercetin markedly upregulated the expression of uncoupling protein 1 (UCP1), a critical thermogenic protein in brown adipocytes, thereby enhancing cellular thermogenic capacity and effectively mitigating glucose and lipid metabolism disorders. Subsequent mechanistic investigations confirmed that quercetin activated the COX2-PGE2-EP4-UCP1 signaling axis by augmenting the stability of cyclooxygenase 2 (COX2) protein, thus mediating its thermogenic-promoting and metabolism-improving effects. This study identifies quercetin as a potential therapeutic agent for the improvement of glucose and lipid metabolism disorders, uncovers a novel molecular mechanism through which quercetin regulates brown adipocyte thermogenesis, and provides a theoretical and experimental foundation for the application of quercetin in the prevention and treatment of obesity and related metabolic diseases.

BackgroundBevacizumab resistance severely limits long-term efficacy in metastatic colorectal cancer (CRC). This study aimed to develop and validate a bevacizumab resistance-associated gene signature for prognosis prediction and immune microenvironment characterization in CRC. MethodsTwo GEO datasets (GSE19862, GSE86582) with bevacizumab response data and TCGA-COAD/READ RNA-seq data were analyzed. Overlapping differentially expressed genes (DEGs) linked to both CRC progression and bevacizumab resistance were identified. An 8-gene signature (AXIN2, PSORS1C1, KRT74, SLC2A3, STIL, IL33, GALNT6, HSD11B2) was constructed via univariate Cox and LASSO-Cox regression. ResultsIn the TCGA cohort, high-risk patients had shorter overall survival (OS; log-rank P < 0.0001). Time-dependent ROC yielded 1-year AUC = 0.638, 3-year AUC = 0.657, and 5-year AUC = 0.757. Multivariate Cox regression confirmed the risk score as an independent prognostic factor. External validation in GSE39582 (optimal cutoff = -1.49) replicated these findings: high-risk patients had inferior OS (P = 0.0016) with acceptable 1/3/5-year AUCs and retained independent prognostic value (HR = 1.634, P = 0.00415). CIBERSORT and ESTIMATE analyses showed that the high-risk group was characterized by increased M2 macrophages and neutrophils, higher immune and stromal scores, and reduced activated memory CD4+ T cells, monocytes, and activated dendritic cells (all P < 0.05). GSEA highlighted enrichment of TNF-/NF-{kappa}B, IL-6/JAK/STAT3, and immune checkpoint pathways in the high-risk group. AXIN2 (HR = 0.829, P = 0.032) was an independent protective factor, while PSORS1C1 (HR = 1.356, P = 0.048) was an independent risk factor. ConclusionThe 8-gene bevacizumab resistance signature robustly predicts prognosis and reflects an immunosuppressive microenvironment closely linked to bevacizumab failure in CRC. These findings provide novel insights into immune-mediated resistance and support clinical risk stratification.

OBJECTIVEThis study aimed to explore the role and underlying mechanism of microRNA-128 (miR-128) in regulating vascular remodeling in spontaneously hypertensive rats (SHRs), focusing on its targeting of peroxisome proliferator-activated receptor {gamma} (PPAR-{gamma}) and modulation of the Toll-like receptor 4/nuclear factor-{kappa}B (TLR4/NF-{kappa}B) inflammatory pathway. METHODSAll experimental procedures were approved by the Animal Care and Use Committee of Fujian Medical University. In vivo, ten-week-old male SHRs were randomly assigned to three groups: renal denervation (RDN, n=6), sacubitril/valsartan (Sac/Val, n=6), and Sham (n=6). Age-matched Wistar-Kyoto (WKY) rats served as normotensive controls (n=6).Eight weeks after intervention, mesenteric arteries were harvested for histological, functional, and molecular analyses. Serum miR-128 levels were measured by quantitative real-time polymerase chain reaction (qRT-PCR). The expression levels of key proteins in the vascular wall were assessed via immunofluorescence (IF), immunohistochemistry (IHC), and Western blotting (WB). Bioinformatics analysis and RNA sequencing (RNA-seq) were employed to identify core genes and signaling pathways associated with hypertension-induced pathological inflammation. RESULTSIn vivo, in the SHR sham-operated group, elevated blood pressure, severe vascular remodeling, and impaired vasodilatory function were observed, accompanied by downregulated miR-128 expression and upregulated TLR4/NF-{kappa}B signaling activity (all p < 0.0001).RDN postoperative, miR-128 expression was significantly restored, which in turn inhibited the TLR4/NF-{kappa}B pathway, reduced the production of pro-inflammatory cytokines (including IL-1{beta}, IL-6, and TNF-), and ameliorated vascular dilation dysfunction in SHRs (all p < 0.0001). Mechanistically, miR-128 negatively regulated the TLR4/NF-{kappa}B signaling pathway while upregulating the expression of PPAR-{gamma} (p < 0.05). CONCLUSIONRDN not only exerts a hypotensive effect but also improves hypertensive vascular remodeling. miR-128 inhibits excessive inflammation in vascular smooth muscle cells and alleviates vascular remodeling in SHRs via the PPAR-{gamma}/TLR4/NF-{kappa}B axis. These findings identify miR-128 as a potential therapeutic target for RDN in the treatment of hypertension, providing a novel regulatory strategy for the precision management of cardiovascular diseases.

Mechanisms that promote organ injury after trauma and hemorrhagic shock (T/HS) remain poorly defined. Endothelial heparan sulfates with a 3-O-sulfate (3-OS) modification, controlled by the HS3ST1 gene, have anticoagulant and anti-inflammatory properties through their interaction with antithrombin. Our objective was to determine whether HS3ST1 deficiency drives organ injury and poor outcomes after T/HS. Hs3st1-/- and wild-type (WT) mice were subjected to T/HS followed by resuscitation with lactated ringers (LR) or fresh frozen plasma (FFP). While no differences were observed between WT and Hs3st1-/- LR resuscitated mice, lung injury and leukocyte infiltrates were significantly increased in FFP resuscitated Hs3st1-/-compared to WT mice. In vitro, leukocyte slow rolling and adherence was increased in HS3ST1 KO compared to WT cells. Among 472 T/HS patients, of which 31 (7%) were homozygous for the rs16881446 variant allele (GG), the number of ventilator free days was lower, and mortality was significantly higher in AG and GG patients. The rs16881446 genotype was independently associated with mortality. In conclusion, HS3ST1 deficiency mitigates organ protection from FFP resuscitation, partly through mediating EC:leukocyte engagement, and predicts mortality after T/HS. These findings identify a novel therapeutic target and prognostic tool that can be leveraged towards improved risk stratification after trauma.

Tuberculosis (TB) remains a formidable global health challenge, exacerbated by the emergence of drug-resistant Mycobacterium tuberculosis strains that threaten to render existing drug therapies and vaccine ineffective. Despite the availability of the Bacillus Calmette-Guerin (BCG) vaccine, its limited efficacy--primarily in infants and young children--falls short of reducing TB prevalence or offering adequate protection to adults. Therefore, developing a new TB vaccine with enhanced efficacy and the capability to generate a robust reservoir of memory cells is essential. Addressing the challenge of drug-resistant tuberculosis requires a deep understanding of bacterial evolution and developing robust countermeasures. This study aims to design a next-generation TB vaccine that provides broad-spectrum protection against various Mycobacterium tuberculosis strains, including drug-resistant ones. By conducting an in-depth investigation into pathogen-human interactions, the research proposes a holistic framework that leverages computational vaccinology to tackle challenges posed by pathogen polymorphism and overcome the limitations of conventional vaccines. By targeting conserved proteins across diverse TB strains and enhancing both humoral and cell-mediated immunity, this study proposes a new strategy for an epitope-based vaccine that provides long-lasting, universal coverage. An extensive proteomic, reverse vaccinology and immunoinformatics analysis of 159 TB strains yielded 27 highly conserved, immunogenic, non-toxic, and non-allergenic epitopes. These epitopes, consisting of 14-cytotoxic T-lymphocytes (CTL), 5-helper T-lymphocytes (HTL), and 8-B-cell epitopes, were used to construct a three-dimensional, multi-epitope TB vaccine designed based on a new concept introduced in this research for maximising vaccine efficacy. Molecular docking and immune simulation studies demonstrated a significant affinity between the vaccine constructs and toll-like receptors, indicating a strong potential for effective immune system engagement. The crucial features of the epitope-based TB vaccine constructed in this research include sequence conservancy, robust antigenicity, exclusion of self-peptides and potential for diverse allelic interactions. The proposed epitope-based vaccine is poised to be highly effective, safe, and capable of providing universal coverage, potentially paving the way for global TB eradication. Validation in laboratory and clinical settings will be essential to confirm its efficacy and real-world applicability.

Abstract Background: Mean platelet volume (MPV) is a simple, low-cost biomarker that reflects platelet activation. Its prognostic value in septic shock remains controversial. We aimed to determine whether MPV at intensive care unit (ICU) admission is associated with hospital mortality in patients with septic shock. Methods: Retrospective cohort study of consecutive adults with septic shock (Sepsis-3 criteria) admitted to a single ICU. MPV, severity scores (SOFA, APACHE II, SAPS II), procalcitonin, and clinical data were collected. The primary outcome was in-hospital mortality. Spearman correlation, univariate and multivariate logistic regression (with Firth's correction), ROC curves, and subgroup analyses were performed. Results: Fifty-eight patients were included; mortality was 58.6%. MPV did not differ between non-survivors and survivors (13.09 {+/-} 1.37 vs. 12.66 {+/-} 1.45 fL, p = 0.259). MPV showed a weak correlation with procalcitonin ({rho} = 0.394, p = 0.002) but not with severity scores. In multivariate analysis adjusting for age, sex, SOFA and comorbidity count, MPV was not an independent predictor of mortality (OR 1.075, 95% CI 0.682-1.755, p = 0.749). The area under the ROC curve for MPV was 0.598 (95% CI 0.444-0.752), significantly lower than that of SOFA (0.837) and procalcitonin (0.836). Subgroup analyses showed no significant association between MPV and mortality in any stratum. Conclusions: In this cohort of septic shock patients, MPV at ICU admission was not associated with hospital mortality and had poor discriminative ability. Widely used severity scores and procalcitonin remain superior prognostic markers. MPV should not be used as a prognostic tool in septic shock. Keywords: Septic shock, Mean platelet volume, Mortality, SOFA, Procalcitonin, Biomarker

Traumatic brain injury (TBI) is a condition of high incidence worldwide, but remains mostly undertreated. Previous observations in preclinical studies pointed to a beneficial effect of insulin-like growth factor 1 (IGF-1) in TBI. As brain injury is associated to loss of IGF-1 sensitivity, we tested the therapeutic potential of AIK3a305 (AIK3), a novel IGF-1 sensitizer. Twenty-four hours after mild TBI induced by controlled impact, mice received daily intraperitoneal injections of AIK3 during 4 weeks. We found that TBI-associated sensorimotor disturbances measured with the adhesive-removal test were reverted by AIK3 treatment. In addition, neurological and cognitive disturbances measured by the neurological severity score and Y maze respectively, were also ameliorated by treatment with the IGF-1 sensitizer, whereas increased anxiety after mild TBI was also normalized by AIK3. Circulating levels of IGF-1 were increased after AIK3 treatment in TBI mice, while serum IL-6 levels, a biomarker of inflammation associated to TBI were similar to control mice treated with AIK3. Transcriptomic analysis determined that treatment with AIK3 widely affected gene expression in TBI brains, showing a general reduction in both up- and down-regulated genes. Collectively, these data support the use of IGF-1 sensitizers such as AIK3 for treatment of TBI.

Spinal cord injury (SCI) is a devastating neurological condition with limited regenerative capacity. Stem cell-based approaches have emerged as promising strategies due to their neuroprotective and immunomodulatory properties, largely mediated by small extracellular vesicles (sEVs) and their molecular cargo, including miRNAs. In this study, we aimed to evaluate the neuroprotective and anti-apoptotic potential of sEVs derived from SPC-01 and iMR-90 neural stem cell sources using an in vitro rat model of SCI. sEVs were isolated from conditioned media and characterized by multi-angle dynamic light scattering and Western blot analysis. Organotypic spinal cord slices (SCS) were used as an in vitro SCI model, with injury induced at 18-20 days, followed by immediate sEV application. After 72 h, tissue samples were collected and tissue was analyzed for markers of apoptosis, cytoskeletal integrity, and survival-related signaling pathways. Results show that SCI induced cytoskeletal disruption and increased apoptotic markers. Treatment with sEVs mitigated these changes, reducing injury-associated protein levels toward baseline. Both SPC-01- and iMR-90-derived sEVs exerted comparable neuroprotective effects, accompanied by decreased PTEN expression, enhanced STAT3 phosphorylation, and increased levels of the anti-apoptotic protein Bcl-xL. In parallel, reduced Nogo-A expression and normalization of RhoA suggested improved cytoskeletal stability and attenuation of inhibitory signaling. Together, these findings demonstrate that neural stem cell-derived sEVs promote early neuroprotective responses in vitro by modulating key signaling pathways, reducing apoptosis, and stabilizing cytoskeletal dynamics, supporting their potential as a cell-free therapeutic strategy for SCI.

Introduction: Calcific aortic stenosis (CAS) is a progressive valvular disease characterized by lipid accumulation, inflammation, and osteogenic remodeling. Emerging evidence implicates gut microbiota-derived metabolites in cardiovascular pathology, yet their contribution to valvular disease remains poorly defined. The aim of this study was to investigate gut microbiota and metabolite signatures in patients with CAS and explore causal relationships using Mendelian randomization (MR). Methods: In a prospective cohort of 54 patients with CAS and 41 age, sex, BMI-balanced non-CAS controls, we performed integrated microbiome and metabolomic profiling. Gut microbial composition was assessed by 16S rRNA sequencing, and circulating levels of tryptophan derivatives, short-chain fatty acids, bile acids, and TMA/TMAO-related metabolites were quantified. MR analyses were performed to assess causal contributions of key metabolic and inflammatory markers to CAS. Results: Baseline characteristics were comparable between groups. CAS patients exhibited a distinct tryptophan metabolic profile, characterized by higher concentrations of inflammatory kynurenine-pathway metabolites and lower indole-3-sulfate. With consistent effect sizes despite modest statistical significance after multiple testing correction. Pathway-level analyses supported preferential routing of tryptophan toward inflammatory host metabolism. In contrast, global microbiota diversity and overall community structure were preserved. However, CAS was associated with depletion of specific Firmicutes taxa, including Eubacterium coprostanoligenes, a key cholesterol-converting bacterium mediating intestinal cholesterol-to-coprostanol transformation. MR analyses suggested LDL cholesterol and lipoprotein(a) as upstream triggers of CAS, whereas ALPL and tryptophan/kynurenine metabolites appear downstream and might reflect systemic inflammation and local metabolic consumption. Sex-stratified analyses revealed enhanced kynurenine pathway activation in males, whereas females exhibited relatively higher TMAO and indole-related metabolites. Conclusion: CAS is characterized by a focused gut-host metabolic reprogramming defined by inflammatory tryptophan catabolism and loss of cholesterol-transforming microbial functions, rather than global dysbiosis. These findings identify a potential gut, valve metabolic axis contributing to valvular calcification, with potential sex-specific effects.

Chlamydia trachomatis is an obligate intracellular Gram-negative pathogen responsible for sexually transmitted infections and trachoma in humans. Although antibiotics are generally effective against acute infections, persistent chlamydial forms often exhibit reduced susceptibility during chronic infection. Chlamydia relies on its type III secretion system (T3SS) to inject effector proteins into host cells, making T3SS proteins attractive targets for antivirulence therapeutics. In this study, we employed an integrated computational pipeline to model and assemble the C. trachomatis T3SS constituent proteins. Template-based modeling using crystallographic structures of homologs from other Gram-negative bacteria revealed a highly conserved structural architecture despite low sequence identity (18-46%). Stereochemical validation confirmed high model quality, with most T3SS proteins exhibiting favorable protein-protein interactions (PPIs). Since the activity of the T3SS complex relies on extensive PPIs, we targeted these PPIs as a promising approach to attenuate bacterial virulence. CdsN, which functions as an ATPase of the T3SS, is a hexamer of which we targeted the dimerization interface. Structure-based virtual screening of compounds from the e-Drug3D and IMPPAT libraries against predicted hotspot residues and the identified druggable pocket at the CdsN dimeric interface, followed by ADMET screening, yielded three promising candidates: M Roflumilast (Drug ID: 1537), Elacestrant (Drug ID: 2081), and Tecovirimat (Drug ID: 1889). All three ligands formed thermodynamically stable complexes with the CdsN dimer, with Elacestrant demonstrating the most favourable binding free energy. This was also confirmed by 100 ns molecular dynamics simulation. This study provides new insights into the molecular architecture of C. trachomatis T3SS and identifies M Roflumilast, Elacestrant, and Tecovirimat as potential drug candidates against chlamydial infection. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/723290v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@1821599org.highwire.dtl.DTLVardef@1581baaorg.highwire.dtl.DTLVardef@1805e98org.highwire.dtl.DTLVardef@c25e56_HPS_FORMAT_FIGEXP M_FIG C_FIG

Bovine tuberculosis (TB), caused by Mycobacterium bovis, has become a global concern over the last two decades. Bovine TB primarily affects cattle, but other domestic livestock are also affected and it is more common in less developed and developing countries. The significant loss of livestock leads to trade restrictions and economic crises. Zoonotic potential of bovine TB raises health concerns for the public. Currently, no effective treatment is available and animal slaughtering is usually undertaken to reduce the burden of it in the environment. Antibiotic therapy can be used on animals living in captivity, but it is not reliable for herd or free-grazing animals. The BCG vaccine is another option available for treating the disease, but it shows limited efficacy in cattle. The prevention of bovine TB is a long-term goal that can only be accomplished by developing a more effective vaccine than BCG and designing new drugs. In this research, we propose therapeutic drug targets and vaccine for treating bovine TB. The conceptual framework for vaccine developed in this study uses a number of bioinformatics approaches to identify potential vaccine candidates and construct an in-silico epitope-based vaccine. Our holistic framework identified potential therapeutic candidates by directly analysing the proteome of TB bacterial strains. Specifically, we performed a comparative proteomic analysis of 11 Mycobacterium bovis strains to cover the diversity and identify conserved proteins among those strains for developing the bovine TB vaccine. An extensive reverse vaccinology and immunoinformatics analysis provided 26 highly immunogenic, non-toxic and non-allergenic epitopes (CTL epitopes-8, HTL epitopes-2 and B-cell epitopes-16) for Mycobacterium bovis required for three-dimensional structure construction of TB vaccine. The constructed epitope-based vaccine showed a potent interaction inside the host, thus generating efficient cell-mediated and humoral immune responses. Next, a framework based on a novel subtractive proteomic approach was developed for identifying bovine TB drug targets. We performed this approach on the 11 Mycobacterium bovis strains and identified nine drug targets that are conserved, essential, antigenic and have unique metabolic pathways in Mycobacterium bovis. These drug targets could further help investigate therapeutic drugs for the treatment of bovine TB. Several bioinformatics prediction tools were used together to ensure checks and balances, aiming to reduce the chance of errors and provide accurate results. The vaccine and drug targets developed in this study can be tested experimentally with confidence for further validation as therapeutics with the potential to eradicate bovine TB globally. The strategies implemented in the study are generic and can be used for other zoonotic infectious diseases. This study would be a game changer in the field of bovine tuberculosis treatment.

The loss of smooth muscle cell (SMC) contractile phenotype contributes to various diseases including atherosclerosis. However, its metabolic basis is not entirely elucidated. Since the transforming growth factor beta (TGF{beta}) signaling is among principal regulators of SMC contractility, we studied metabolic regulation of TGF{beta} signaling in SMCs in vitro and atherosclerotic mouse models and human lesions. We found that TGF{beta} induced Ac-CoA synthetase 2 (ACSS2)-dependent Ac-CoA production, by suppressing pyruvate dehydrogenase kinase 4 (PDK4). This stabilized R-SMADs and TGF{beta} receptor 1, preserving SMC contractile phenotype. SMC-specific PDK4 knockout mimicked the effect of TGF{beta} signaling both metabolically and phenotypically, increasing glucose-derived synthesis of Ac-CoA and SMC contractile phenotype. SMC-specific Pdk4 knockout in ApoE knockout mice reduced atherosclerosis. Furthermore, human specimens demonstrated a strong correlation between PDK4 level and atherosclerosis severity. These findings indicate that continuous TGF{beta} signaling, critical to the maintenance of the normal SMC contractile state and is regulated by PDK4 and carbohydrate metabolism. TeaserReducing PDK4 metabolically restricts aortic plaque growth via TGF{beta}-dependent SMC contractility.

Persistence of HIV antigens may drive chronic inflammation, leading to early-onset comorbidity among people living with HIV. We found that the presence of soluble glycoprotein 120 in plasma is associated with increased coronary inflammation, as measured by the pericoronary fat attenuation index (PFAI), a predictor of overt cardiovascular disease.

Orthoflavivirus, such as West Nile Virus (WNV), dengue virus (DENV) and ZIKA virus (ZIKV), are globally distributed pathogens that pose substantial threats to human health. Currently, there are still no effective antiviral drugs for WNV or ZIKV. Despite the availability of two licensed DENV vaccines, their use remains limited due to potential risks, highlighting an urgent need for antiviral drug development. The highly conserved orthoflavivirus protease NS2B/NS3 is required for viral replication, making it a promising anti-flavivirus target. A major challenge, however, is the highly charged active site of this enzyme, which requires charged chemical matters with low bioavailability. An alternative and more attractive strategy is to target potential allosteric sites or folding intermediate states of the protease. In this work, we employ the topology-based coarse-grained G[o] modeling to explore the coupled binding and folding pathways of WNV NS2B/NS3 protease and study the effects of the widely used experimental construct with a G4SG4 linker between NS2B and NS3 on stability and folding. Our results provide a holistic conformational landscape of the protease binding and folding, including several key intermediate states. We find that the presence of the G4SG4 linker alters the folding pathways and destabilizes the NS2B C-terminus. The latter is consistent with experimental observations that the G4SG4 linked protease has lower activity and adopts an open state without the substrate in crystal structures. Together, these findings provide for the first time a complete picture of the binding and folding of the NS2B/NS3 protease and identify important folding intermediate states that could be targeted for allosteric antiviral drug development. TOC Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/722635v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@163c356org.highwire.dtl.DTLVardef@ad7b35org.highwire.dtl.DTLVardef@173ed8aorg.highwire.dtl.DTLVardef@1f026bf_HPS_FORMAT_FIGEXP M_FIG C_FIG

Inflammation and oxidative stress (OS) are key to Parkinsons disease (PD). We performed a cross-dataset integrative transcriptomic analysis to identify OS- and inflammation-related hub genes persistently dysregulated in PD and to evaluate their response to nutrigenomic interventions using publicly available datasets. Four GEO datasets (GSE7621, GSE20141, GSE20146, GSE49036) were analysed to identify differentially expressed genes (DEGs), which were intersected with GeneCards OS-inflammation gene sets. Functional enrichment analyses, including gene ontology (GO), pathway over-representation analysis (ORA), and protein-protein interaction (PPI) analysis, were used to identify key pathways and hub genes. Gene-food bioactive compound (FBC) association was explored by integrating PD signatures with nutrigenomic profiles from NutriGenomeDB. We identified 183 DEGs in PD, enriched in synaptic, dopaminergic, OS, and inflammatory pathways. Intersection analysis yielded 26 OS-inflammation-related genes and 10 central regulators, including TH, DDC, SNCA, LRRK2, HSPB1, and HSPA1B. revealed opposing transcriptional patterns, with several FBCs suppressing stress-related genes and upregulating dopaminergic markers such as TH, GCH1, and DDC. Overall, this integrative analysis highlights OS-inflammation gene networks in PD and identifies candidate diet-gene interactions that warrant further experimental validation

BackgroundTrained immunity is a durable functional reprogramming of innate immune cells characterized by enhanced responsiveness upon secondary challenge. While metabolic rewiring and epigenetic remodeling are well-established features of this process, the contribution of ubiquitin-mediated post-translational regulation remains poorly defined. MethodsWe performed an integrative analysis of publicly available human transcriptomic datasets derived from monocytes, macrophages, and PBMCs exposed to established training stimuli ({beta}-glucan, Bacillus Calmette-Guerin [BCG], and hemin-{beta}-glucan) followed by secondary stimulation. A curated panel of deubiquitinating enzymes (DUBs) and E3 ubiquitin ligases with established immune functions was analyzed for differential expression. Gene Ontology (GO) and KEGG pathway enrichment analyses were conducted to evaluate higher-order convergence across independent datasets. ResultsAcross multiple trained immunity models, we identified reproducible transcriptional remodeling of ubiquitin-modifying enzymes. USP25, OTUB1, and TRIM25 were consistently upregulated following restimulation, whereas several chromatin- and cytokine-regulatory DUBs--including USP3, USP4, USP7, USP16, MYSM1, and USP38--were downregulated. Normalization to RPMI-restimulated controls reduced many activation-associated signals; however, USP25 remained persistently elevated, suggesting a stable training-associated signature. Pathway enrichment analysis independently demonstrated significant engagement of ubiquitin-related functional categories across datasets, supporting coordinated reorganization of ubiquitin regulatory networks. ConclusionThese findings identify selective transcriptional remodeling of the ubiquitin- proteasome system as a recurring feature of trained immunity. Integrating ubiquitin signaling into the established metabolic-epigenetic framework expands the conceptual model of innate immune memory and suggests that ubiquitin-modifying enzymes function as modulatory rheostats shaping immune amplitude and stability. Future functional and proteomic studies are required to determine whether these transcriptional signatures directly mediate trained immunity phenotypes.

Influenza A virus (IAV) causes significant morbidity and mortality worldwide. Understanding how viral RNAs may regulate host genes through microRNA-like mechanisms can clarify pathogenesis and reveal therapeutic targets. In this study, we screened all eight IAV H3N2 RNA segments (PB2, PB1, PA, HA, NP, NA, M, and NS) using an ab initio computational pipeline; five segments (PB2, PB1, PA, HA, and M) met the VMir scoring threshold for further analysis, while NP, NA, and NS were excluded due to low pre-miRNA scores. Mature miRNAs were identified using MatureBayes, and target genes in the human genome were predicted with the miRDB server. From these targets, we selected two genes per qualifying segment (10 genes total) based on their functional relevance to influenza infection and supporting literature; all selected genes are unique to their respective segment. We identified 10 segment-specific target genes (IFNL1, DDX60, SAMHD1, MAVS, IRF4, BIRC2, AGO1, MAP3K1, NOD1, and TNFAIP1) and one common target across all five analyzed segments (CADM2). Gene Ontology and pathway analyses showed enrichment in interferon signaling, RIG-I-like receptor pathways, antiviral restriction, RNA interference, and inflammatory responses. Literature supports roles for these genes in pulmonary and antiviral innate immunity. Our findings provide a basis for experimental validation and may help the research community better understand influenza virus pathogenesis and identify novel therapeutic candidates. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/725090v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@2b14adorg.highwire.dtl.DTLVardef@5a9b2eorg.highwire.dtl.DTLVardef@81ffc1org.highwire.dtl.DTLVardef@be119b_HPS_FORMAT_FIGEXP M_FIG C_FIG

Clot resistance to pharmacological thrombolysis remains a critical challenge in ischemic stroke (IS) management. Thrombus heterogeneity, particularly the presence of thrombolysis-resistant domains composed of dense fibrin and non-fibrin components, including neutrophil extracellular traps (NETs), significantly limits the efficacy of recombinant tissue-type plasminogen activator (r-tPA) and its variant, Tenecteplase (TNK). Consequently, novel therapeutic strategies are urgently required. Emerging evidence suggests that co-administration of deoxyribonuclease I (DNase I) with r-tPA can degrade DNA fibers and enhance clot lysis. In this study, we optimized a previously developed theranostic agent--iron oxide microparticles coated with polydopamine--by dual-grafting both r-tPA and DNase to target resistant thrombi. Using functional ultrasound imaging (fUS) during the acute phase of IS, we demonstrated accelerated reperfusion with this dual-functionalized platform in a r-tPA resistant IS model. Furthermore, MRI analysis confirmed a significant reduction in lesion volume at 24 hours, correlating with improved functional recovery five days post-ischemia.

Primary human bronchial epithelial cells (pHBECs) of the airways of smokers are chronically exposed to cigarette smoke, which may induce chronic obstructive pulmonary disease (COPD) ranked fourth among the most common global causes of death. Using an established protocol for differentiation of pHBECs to a pseudostratified epithelium at an air liquid interface (ALI), we analyzed functional expression of transient receptor potential vanilloid 4 (TRPV4) proteins after application of cigarette smoke extract (CSE), which upregulated seven smoke exposure regulated genes (SERGs). TRPV4 protein expression in the plasma membrane and localization next to the cilia of ciliated cells was reduced, while cell barrier function was not altered after chronic exposure to CSE for 28 days compared to untreated control cells. Accordingly, TRPV4-mediated Ca2+ influx was blocked in pHBECs after CSE exposure. Moreover, Os-9 protein, which after binding mediates protection from degradation of TRPV4 protein by polyubiquitination, was significantly less expressed in pHBECs upon CSE exposure. Most interestingly, overexpression of OS-9 in pHBECs rescued reduced TRPV4 protein levels induced by CSE. Our study identifies a novel molecular mechanism of toxicity by CSE interfering with TRPV4 and OS-9 expression in pHBECs, which may blaze the trail for new therapeutic options in COPD.