Search Results (315)

Cellular senescence, characterized by permanent cell cycle arrest, significantly influences cancer development, immune regulation, and progression. However, the precise mechanisms by which senescence contributes to colorectal cancer prognosis remain to be fully elucidated. By integrating expression profiles of senescence-related and prognostic genes in colon adenocarcinoma (COAD) patients, we formulated and confirmed a nine-gene cellular senescence-related signature (CSRS) that integrates senescence-associated and prognosis-predictive genes using data from the CellAge, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). A cell senescence-related prognostic formula was developed as follows: CSRS = (CASP2 × 0.2098) + (CDKN2A × 0.1196) + (FOXD1 × 0.1472) + (ING5 × 0.3723) + (OXTR × 0.0786) + (PHGDH × 0.1408) + (SERPINE1 × 0.1127) + (SNAI1 × 0.1034) + (LIMK1 × 0.0747). In a multivariate Cox proportional hazards model, the CSRS score, age and TNM stage were all identified as significant independent indicators for overall survival, affirming their prognostic value in colorectal cancer. The CSRS-high group exhibited significantly up-regulated senescence-associated secretory phenotype (SASP) and immune cell infiltration, whereas the CSRS-low group showed an apparent better response to immune-checkpoint inhibitor therapy. Our findings suggest CSRS score and its constituent genes represent potential biomarkers for prognosis and immunotherapeutic benefit in COAD patients. Extending this nine-gene set into a broader senescence-associated panel should be a next step toward delivering truly individualized treatment plans. Full article

Sharp declines in temperature pose a significant risk for mass mortality events in the Chinese soft-shelled turtle (Pelodiscus sinensis). To assess the effects of acute cold stress on intestinal health, turtles were exposed to temperatures of 28 °C (control), 14 °C, and 7 °C for 1, 2, 4, 8, and 16 days. The results showed that acute cold stress at 14 °C and 7 °C induced time-dependent alterations in intestinal morphology and histopathology. The damage was more severe at 7 °C, characterized by inflammatory cell infiltration, lymphoid hyperplasia, and extensive detachment and necrosis across the villi, muscle layer, and submucosa. 16S rDNA sequencing revealed significant shifts in intestinal microbiota composition in the 7 °C group, dominated by Helicobacter and Citrobacter. Transcriptomic analysis identified differentially expressed genes (DEGs) that respond to acute cold stress and are involved in the Toll-like receptor signaling pathway (Tlr2, Tlr4, Tlr5, Tlr7, and Tlr8), the NOD-like receptor signaling pathway (Traf6, Traf2, Casr, Rnasel, Pstpip1, Plcb2, Atg5, and Mfn2), apoptosis (Tuba1c, Ctsz, Ctsb, Kras, Hras, Pik3ca, Bcl2l11, Gadd45a, Pmaip1, Ddit3, and Fos), and the p53 signaling pathway (Serpine1, Sesn2, Ccng2, Igf1, Mdm2, Gadd45a, Pmaip1, and Cdkn1a). Metabolomic profiling highlighted differentially expressed metabolites (DEMs) that cope with acute cold stress, such as organic acids (oxoglutaric acid, L-aspartic acid, fumaric acid, DL-malic acid, and citric acid) and amino acids (including L-lysine, L-homoserine, and allysine). The integrated analysis of DEGs and DEMs underscored three key pathways modulated by acute cold stress: linoleic acid metabolism, neuroactive ligand–receptor interaction, and the FoxO signaling pathway. This study provides a comprehensive evaluation of intestinal health in Chinese soft-shelled turtles under acute cold stress and elucidates the underlying mechanisms. Full article

Hypoglycemia is associated with cardiovascular events reflected by platelet abnormalities. We hypothesized that sequential endothelial changes may occur during hypoglycemia that may enhance cardiovascular risk. In type 2 diabetes (T2D) (n = 23) and controls (n = 23), blood SOMAscan proteomic analysis of endothelial proteins at baseline, insulin-induced hypoglycemia and post hypoglycemia to 24 h were examined using repeated-measures linear mixed modeling with a prospective parallel study design. Most endothelial proteins that changed over time did not differ between groups. Baseline levels of P-selectin, plasminogen activator inhibitor-1 (PAI-1; serpine-1), E-selectin and angiopoietin-1 (ANGPT1) were significantly higher, whilst cadherin-5 was lower in T2D. Several proteins exhibited changes versus baseline in both T2D and controls. Under hypoglycemia, decreases in cadherin-5 and soluble angiopoietin-1 receptor (sTie-2) were observed, with increased P-selectin, intercellular adhesion molecule-3 (ICAM3), ANGPT1 and PAI-1. Post hypoglycemia, decreased cadherin-5 and ICAM5 were observed at 2 h and PAI-1 at 4 h, as well as increases in P-selectin at 30 min, 1 h and 24 h and ICAM3 at 24 h. Post hypoglycemia, E-selectin, P-selectin and ICAM3 were significantly lower in T2D patients at 2 h, while PAI-1 was significantly lower at 4 h and ICAM3 was significantly lower at 24 h. Baseline endothelial proteins differed between T2D and controls, which may suggest local endothelial inflammatory activation leading to a pro-thrombotic, destabilized vascular phenotype characteristic of diabetic vasculopathy. Hypoglycemia may exacerbate this towards a pro-adhesive and pro-thrombotic phenotype, worsening endothelial dysfunction. Full article

Cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) have transformed the treatment landscape for estrogen receptor-positive (ER+) breast cancer, yet resistance remains a major clinical challenge. Although CDK4/6i induce G₁ arrest and therapy-induced senescence (TIS), the exact nature of this senescent state and its contribution to resistance are not well understood. To explore this, we developed palbociclib- (2PR, 9PR, TPR) and abemaciclib- (2AR, 9AR, TAR) resistant ER+ breast cancer sublines through prolonged drug exposure over six months. Resistant cells demonstrated distinct phenotypic alterations, including cellular senescence, reduced mitochondrial membrane potential, and impaired glycolytic activity. Cytokine profiling and enzyme-linked immunosorbent assay (ELISA) validation revealed a non-canonical senescence-associated secretory phenotype (SASP) characterized by elevated growth/differentiation factor 15 (GDF-15) and serpin E1 (plasminogen activator inhibitor-1, PAI-1) and absence of classical pro-inflammatory interleukins, including IL-1α and IL-6. IL-8 levels were significantly elevated, but no association with epithelial–mesenchymal transition (EMT) was observed. Resistant cells preserved their epithelial morphology, showed no upregulation of EMT markers, and lacked aldehyde dehydrogenase 1-positive (ALDH1+) stem-like populations. Additionally, Regulated upon Activation, Normal T-cell Expressed, and Secreted (RANTES) was strongly upregulated in palbociclib-resistant cells. Together, these findings identify a distinct, non-canonical senescence phenotype associated with CDK4/6i resistance and may provide a foundation for identifying new vulnerabilities in resistant ER+ breast cancers through targeting SASP-related signaling. Full article

Environmental allergens trigger epithelial reactive oxygen species (ROS) production and cellular senescence, contributing to airway inflammation. The aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor responsive to environmental stimuli, may modulate this process. Single-cell transcriptomics from allergen-challenged bronchoalveolar brushings of allergic asthma and non-asthmatic allergic control subjects were analyzed for ROS, senescence, and AhR activity. Club cell-specific p16 knockout (p16^ΔScgb1a1) and AhR-deficient (AhR^ΔScgb1a1) mice were used to assess epithelial senescence and AhR function. Single-cell analysis revealed epithelial senescence as a hallmark of allergen-induced asthma. p16^ΔScgb1a1 mice exhibited reduced ROS levels and airway inflammation. Single-cell analysis also demonstrated increased AhR activity and ROS generation in airway epithelial cells of allergen-treated asthmatics, and ROS correlated positively with AhR activity and senescence. It was documented that the regulation of AhR on senescence was attenuated by VAF347, whereas AhR deficiency exacerbated ROS generation and inflammation in AhR^ΔScgb1a1 mice. RNA-seq identified senescence as a key AhR-regulated pathway, implicating c-Myc, TGF-β2, and SERPINE1 as major targets. AhR binding to the c-Myc promoter was confirmed by ChIP-PCR, and pharmacologic inhibition of c-Myc with EN4 reduced allergen-induced ROS, senescence, and inflammation. These findings demonstrate that epithelial AhR suppresses allergen-induced ROS generation and cellular senescence via direct regulation of c-Myc. Full article

Parasitoid wasp venoms represent highly specialized biochemical arsenals that evolved to manipulate host physiology and ensure successful development of the parasitoid offspring. However, the molecular targets and mechanisms underlying this complex host modulation remain poorly understood. To address this, we employed an AI-driven discovery pipeline, integrating the sequence-based predictor D-SCRIPT with the structural modeler AlphaFold3, to characterize LjSPI-1, a venom serpin from Liragathis javana. This computational workflow highlighted a previously unreported candidate partner—a host serine carboxypeptidase (Chr09G02510). Crucially, we detected a direct physical interaction between these two proteins through both in vitro pull-down and in vivo yeast two-hybrid assays, supporting this AI-prioritized interaction under experimental conditions. Our study identifies a high-priority molecular pairing and demonstrates the utility of an AI-guided strategy for uncovering candidate targets of venom proteins. In addition, guided by the predicted biochemical role of Chr09G02510, we propose several plausible physiological hypotheses linking this interaction to host peptide metabolism and immune modulation. These hypotheses serve as a conceptual basis for future mechanistic and toxicological investigations. Full article

This study employed an integrated network toxicology and molecular docking approach to explore the molecular mechanisms by which the herbicide 2,4-Dichlorophenoxyacetic acid (2,4-D) may contribute to neurodegenerative diseases (NDDs). We identified 89 common targets through the intersection of potential 2,4-D-related targets and NDD-associated genes. Among these, 12 core targets—including NFKB1, PPARG, SERPINE1, NOS3, and NFE2L2—were highlighted via protein–protein interaction network analysis. Functional enrichment revealed that these targets are involved in key pathways such as inflammatory response, oxidative stress, metabolic dysregulation, and synaptic dysfunction. Molecular docking further confirmed strong binding affinities between 2,4-D and all core targets (binding energy ≤ −5.1 kcal·mol⁻¹). These findings systematically reveal, for the first time, a multi-target and multi-pathway mechanism through which 2,4-D may induce neuronal injury, providing a theoretical basis for assessing environmental risk in neurodegeneration. Full article

Background: Vaspin (also known as serpinA12) is a recent discovery among adipokines. It plays a significant role in obesity-related conditions, many of which are classified as chronic, inflammatory or lifestyle diseases. Due to its anti-inflammatory and insulin-sensitizing properties, vaspin has been investigated as a biomarker and potential therapeutic agent. Methods: A literature review was conducted using the MEDLINE and SCOPUS databases using the phrases “vaspin” and “serpinA12” to summarize the most recent and influential research concerning vaspin’s mechanisms and influence on various tissues. Results and Conclusions: Vaspin is notably involved in metabolic syndrome, and it is generally associated with mitigating conditions like insulin resistance and obesity-related chronic inflammation. In addition, its beneficial effects on endothelial and smooth muscle cells under hyperglycemic and hyperlipidemic conditions are also well documented. There is growing evidence that vaspin positively impacts cardiovascular health, reducing the risk of ischemic stroke and the development of atherosclerosis. Moreover, some studies suggest a direct influence of vaspin on the central nervous system, with its administration shown to reduce the expression of neuropeptide Y, a key regulator of food intake. Many of the reviewed sources highlight vaspin not only as a possible biomarker but also as a promising therapeutic candidate. However, despite intensive research on vaspin over the past 20 years, there are significant disparities between animal and in vitro studies versus human studies. A further limitation in the field is the lack of standardization in research methodologies, which contributes to inconsistent and sometimes contradictory results. Full article

Background: Recurrent pregnancy loss (RPL) is a multifactorial condition in which genetic variants associated with thrombophilia may contribute to altered coagulation and adverse pregnancy outcomes. Objective: This study aimed to investigate the association between thrombophilia-related single nucleotide variants (SNVs) and coagulation-related metabolites in a cohort of Mexican women with RPL. Methods: A retrospective and descriptive design was conducted including 105 women with at least two consecutive miscarriages and with a multidisciplinary approach that included a thrombophilia-associated SNVs panel. Peripheral blood samples were collected after fasting for biochemical and molecular analyses. Genotyping of thrombophilia-associated SNVs was performed using real-time PCR with custom-designed TaqMan probes on a Rotor-Gene Q platform, including variants in AGT (rs4762, rs699), F7 (rs6046), FGB (rs1800790), MTR (rs1805087), MTRR (rs1801394), MTHFR (rs1801133, rs1801131), F2 (rs1799963), F5 (rs6025), SERPINE1 (rs1799889), F12 (rs1801020), and F13A1 (rs5985) genes. Coagulation parameters evaluated were folic acid, cobalamin, fibrinogen, D-dimer, homocysteine, antithrombin III activity, thrombin time (TT), prothrombin time (PT), activated partial thromboplastin time (aPTT), international normalized ratio (INR), and Factor XII activity. Results: Significant differences were found in INR values across F7-rs6046 genotypes (p = 0.006), with an additive model showing a mean difference of 0.05 (p = 0.0009). The F12-rs1801020 variant was strongly associated with Factor XII activity (p = 0.002) and aPTT (p = 0.045). Conclusions: These findings indicate that F7-rs6046 and F12-rs1801020 genotypes influence specific coagulation parameters, suggesting that certain thrombophilia-associated SNVs may modulate the hemostatic profile in Mexican women with RPL and contribute to personalized risk assessment in reproductive medicine. Full article

Background/Objectives: Previous studies have demonstrated an association between migraine headache and temporomandibular joint disorders (TMDs), with a higher prevalence of TMD symptoms in patients with migraine. Methods: In this study, we conducted RNA sequencing to identify differentially expressed genes (DEGs) in the spinal trigeminal nucleus caudalis of mice with migraine-like pain and/or myogenic TMD. Results: We observed 204 upregulated and 274 downregulated genes in the comorbid migraine and TMD group compared to the control group. We identified 15 ferroptosis-related DEGs enriched in the pathways of neurodegeneration, cellular homeostasis, interleukin signaling, and pain response. Gene Ontology analysis highlighted the involvement of neuroinflammatory response and monoamine transmembrane transporter activity, while Gene Set Enrichment analysis showed enrichment in chemokine signaling, cell cycle, and calcium signaling pathways. Immune infiltration analysis identified M0 macrophages, immature dendritic cells, neutrophils, and eosinophils as key responders. Hub genes in the protein–protein interaction network included Gm7536, Rpl17, Rpl22l1, Rpl14, Rps8, Rps29, Rpl35, Gm4889, Gm11808, Rps27rt, Rps12-ps3, Rpl10-ps3, Gm9843, Oas1c, Il1b, and Serpine1, indicating their synergistic roles in such orofacial pain comorbidity. Conclusions: Our results suggest that the comorbid migraine and TMD can regulate gene expressions involving ferroptosis and immune cell responses and the identified DEGs could be targeted to develop novel therapies for this painful comorbidity. Full article

Inherited retinal degenerations (IRDs), driven by pathogenic mutations, often involve primary dysfunction of the retinal pigment epithelium (RPE)—a pathogenic feature shared with atrophic age-related macular degeneration (aAMD), despite aAMD’s multifactorial etiology. Prominin-1 (Prom1), traditionally linked to photoreceptor pathology, has an unclear role in RPE homeostasis. We assessed Prom1 expression in C57BL/6J mouse retina sections and RPE flat mounts using immunohistochemistry and generated Prom1-knockout (KO) mouse RPE cells via CRISPR/Cas9. Bulk RNA sequencing with DESeq2 and gene set enrichment analysis (GSEA) revealed Prom1-regulated pathways. Prom1-KO cells exhibited upregulation of Grem1, Slc7a11, Serpine2, Il1r1, and IL33 and downregulation of Ablim1, Cldn2, IGFBP-2, BMP3, and OGN. Hallmark pathway interrogation identified reduced expression of PINK1 (mitophagy) and MerTK (phagocytosis), implicating defects in mitochondrial quality control and outer segment clearance. Enrichment analysis revealed activation of E2F/MYC targets, mTORC1 signaling, oxidative phosphorylation, and TNFα/NF-κB signaling, alongside suppression of apical junctions, bile acid metabolism, and Epithelial-Mesenchymal Transition (EMT) pathways. These findings suggest Prom1 safeguards RPE integrity by modulating stress responses, mitochondrial turnover, phagocytosis, metabolism, and junctional stability. Our study uncovers Prom1-dependent signaling networks, providing mechanistic insights into RPE degeneration relevant to both IRD and aAMD, and highlights potential therapeutic targets for preserving retinal health. Full article

The common carp Cyprinus carpio L. is a cornerstone aquaculture species, yet transcriptome interpretation is complicated by its paleotetraploid genome and extensive alternative splicing. A species-tailored oligonucleotide microarray was developed to deliver reproducible, gene-level expression profiling. Probe design was anchored to the SPL01 reference and implemented on an Agilent platform using a gene-level strategy that collapsed transcripts to genes, selected the longest isoform, and placed 3′-anchored 60-mer probes. The workflow incorporated embedded technical controls and a standardized two-color pipeline to ensure stable measurements across arrays. Baseline functional organization of the head kidney was defined using 614 C. carpio L. -Danio rerio orthologs and complementary enrichment tools. Coherent signatures emerged for hemoglobin-mediated oxygen transport, heme and porphyrin metabolism, antioxidant defense driven by peroxiredoxin and thioredoxin systems, including hydrogen peroxide detoxification, protease regulation through SERPIN, SPINK, and WFDC families, and elements of innate and humoral immunity. Targets bearing c-Myc motifs showed a modest positive bias consistent with ongoing hematopoiesis. These resolved baseline modules provide a reference against which infection- or exposure-induced programs such as interferon-stimulated genes, chemokines and chemotaxis, complement activation, and degranulation can be detected and quantified. The platform complements RNA-seq by offering cost-efficient, rapid, and comparable measurements suited to large cohorts and longitudinal designs. Anticipated applications include host–pathogen studies for viral and bacterial agents and the assessment of chemical contaminants in aquaculture surveillance, supporting standardized, cross-study decision-making in research and health monitoring. Full article

The activity of serpins uses a specific mechanism or process. This process comprises several steps and is related to significant structural changes that involve significant displacement of chain fragments and whole molecules of protease. An important role is played by a segment of the serpin chain called the Reactive Central Loop (RCL), which interacts with the protease by inhibiting its activity. For the covalent binding of the protease to serpin, the movement of the protease molecule is an effect of splicing the RCL segment into beta-sheet A of serpin. There are structural forms—native, latent, Michaelis complex (non-covalent enzyme-inhibitor complex prior to RCL cleavage), covalent serpin–protease complex, and cleaved—associated with serpin activity. In this work, all these structural forms are discussed using the fuzzy oil drop (FOD-M) model, where the assessment criterion of structuring is based on identifying the type of hydrophobicity distribution. The analysis reveals the specificity of the inhibition mechanism, including the specific action of the RCL. The structural changes involved in this process have been shown to preserve the distribution of hydrophobicity in the form preferred by the aqueous environment in which serpins are active. The disorder (according to FOD-M model) in two complexes (Michaelis and covalent) is hypothetically treated as code for degradation factors. The applied model assesses the function-related structures using the hydrophobicity distribution as the criterion in contrast to many publications based on energetic aspects of serpin activity. Structural changes appear appropriate for water environments—the environment of serpin activity. Full article

The formation of the Chinese three-keeled pond turtle (Mauremys reevesii) carapace is a complex biological event involving developmental processes such as collagen deposition and ossification. As a key regulator of collagen deposition and ossification, Col10a1 may play a crucial role in carapace development, though its specific mechanism remains unclear. To investigate the role of Col10a1 during carapace development and its regulatory mechanisms, we cloned its cDNA sequence and performed bioinformatic analysis. This revealed that Col10a1 encodes a stable, hydrophilic, and basic protein, with phylogenetic analysis showing closest evolutionary relationships to other reptiles and the greatest divergence from fish. Further RT-qPCR analysis examined Col10a1 expression patterns in M. reevesii embryos at stages 14, 18, and 22, as well as in various tissues of adult males and females. Results indicated that during embryonic development, Col10a1 expression levels progressively increased alongside the progression of carapace ossification and collagen deposition, suggesting its involvement in regulating this process. In adult tissues, Col10a1 exhibited widespread expression, with particularly high levels in the brain, kidneys, and liver, suggesting potential specialized functions in these organs. Finally, in vitro experiments demonstrated that inhibition of the Wnt/β-catenin pathway with salinomycin sodium salt downregulated the expression of both its target genes (Sp5, Myc, Ccnd1) and Col10a1. In contrast, inhibition of the TGF-β/Smad pathway with oxymatrine suppressed its target genes (Serpine1, Cdkn1a) but concomitantly upregulated Col10a1. These results suggest that Col10a1 expression may be positively regulated by the Wnt/β-catenin pathway and negatively regulated by the TGF-β/Smad pathway. Our findings provide novel insights into the molecular mechanisms governing carapace development and collagen deposition in M. reevesii, laying a crucial foundation for further investigations into the regulatory networks involving Col10a1 during carapace formation. Full article

Laquinimod (LAQ) and interferon-β1a (IFN-β1a, Rebif) are immunomodulatory therapies for relapsing–remitting multiple sclerosis (RRMS) that may also influence vascular and hemostatic pathways. This study investigated transcriptional regulation of coagulation- and fibrinolysis-related genes in peripheral blood mononuclear cells (PBMCs) from LAQ- and IFN-β1a–treated RRMS patients. In the LAQ cohort, within-subject paired analysis revealed significant downregulation of procoagulant and antifibrinolytic transcripts, including F2, F10, SERPINE1 (PAI-1), and TFPI, after six months of treatment (FDR < 0.01, |fold change| ≥ 1.5). These findings suggest that LAQ exerts an anticoagulant and antifibrinolytic transcriptional effect, potentially mediated through aryl hydrocarbon receptor (AhR) signaling. Western blot analysis confirmed decreased PAI-1 protein expression. In contrast, IFN-β1a treatment induced a distinct transcriptional pattern. Genes associated with fibrinolysis and endothelial stabilization (THBD, ANXA2, SERPINA1) were upregulated, while procoagulant mediators (F2R, F13A1, PROS1) were downregulated. Correlation analysis demonstrated significant relationships between interferon-inducible genes and coagulation-related transcripts, suggesting coordinated regulation between type I interferon signaling and vascular pathways. Collectively, these results indicate that LAQ and IFN-β1a exert opposing yet convergent influences on coagulation and fibrinolytic networks in immune cells. Both therapies modulate transcriptional regulators of vascular homeostasis, revealing a potential molecular interface between immune modulation and hemostatic balance in RRMS. These findings are exploratory and hypothesis-generating, warranting further functional and clinical validation. Full article