Search Results (3,456)

Introduction: Neuroinflammation is a common pathological hallmark of Coronavirus Disease 2019 (COVID-19) and epilepsy; however, their shared immunogenomic mechanisms remain poorly defined. This study explores shared immune-inflammatory transcriptomic signatures and identifies potential repositioning therapeutics. Methods: We integrated single-cell RNA-seq data from peripheral blood mononuclear cells (PBMCs) of COVID-19 patients and healthy donors (GSE149689), and bulk RNA-seq data from hippocampal tissue of patients with Temporal Lobe Epilepsy with Hippocampal Sclerosis (TLE-HS) and healthy controls (GSE256068). Common Differentially Expressed Genes (DEGs) were identified and subjected to GO/KEGG enrichment, a PPI network, hub gene detection (cytoHubba), and transcriptional regulation analysis (ENCODE-based TF/miRNA networks). Drug repositioning was performed using the LINCS L1000 database. Results: We identified 25 DEGs shared across datasets, including 22 upregulated genes enriched in cytokine–cytokine receptor interaction, NF-κB, and Toll-like receptor pathways. PPI analysis revealed a CX3CR1–TLR4-centered immune module. Gabapentin emerged as a promising repositioning candidate with potential to downregulate CX3CR1, TLR4, and selectin P ligand (SELPLG). Receiver Operating Characteristic (ROC) analysis confirmed the diagnostic value of these targets (AUC > 0.90 in epilepsy). A mechanistic model was proposed to illustrate Gabapentin’s dual action on microglial polarization and cytokine suppression. Conclusions: Our results reveal a shared CX3CR1–TLR4–NF-κB inflammatory axis in COVID-19 and epilepsy, supporting Gabapentin as a potential dual-action immunomodulator. These findings reveal a previously underappreciated immunomodulatory role for Gabapentin, providing mechanistic rationale for its repositioning in neuroinflammatory conditions beyond seizure control. Full article

Understanding the mechanical behavior of implanted neural electrode arrays is crucial for BCI development, which is the foundation for ensuring surgical safety, implantation precision, and evaluating electrode efficacy and long-term stability. Therefore, a reliable FE models are effective in reducing animal experiments and are essential for a deeper understanding of the mechanics of the implantation process. This study established a novel finite element model to simulate neural electrode implantation into brain tissue, specifically characterizing the nonlinear mechanical responses of brain tissue. Synchronized electrode implantation experiments were conducted using ex vivo porcine brain tissue. The results demonstrate that the model accurately reproduces the dynamics of the electrode implantation process. Quantitative analysis reveals that the implantation force exhibits a positive correlation with insertion depth, the average implantation force per electrode within a multi-electrode array decreases with increasing electrode number, and elevation in electrode size, shank spacing, and insertion speed each contribute to a systematic increase in insertion force. This study provides a reliable simulation tool and in-depth mechanistic analysis for predicting the implantation forces of high-density neural electrode arrays and offer theoretical guidance for optimizing BCI implantation device design. Full article

Background: Zebrafish-based drug discovery systems provide significant advantages over mammalian models for high-throughput in vivo screening. Among these, the NF-κB eGFP reporter system significantly enhances drug discovery in zebrafish by enabling real-time, high-resolution monitoring of pathway activity in live organisms, thereby streamlining mechanistic studies and high-throughput screening. Methods: We developed a novel AI (Quantifish and Orange software)-based zebrafish precision individualized 96-well ZF plates (0–7 dpf) and individualized MT tanks (8 dpf–4 mpf) protocol for the transposon-mediated transgenesis of the NFκB eGFP reporter system. Results: One-cell stage embryos were administered NFκB reporter construct and Tol2 transposase mRNA via microinjection and transferred to separate wells of a 96-well ZF plate. Bright-field and fluorescence images of each well were captured at 5 dpf in the F0, F1, and F2 generations using the automated confocal high-content imager CQ1. The Quantifish software was used for the automated detection and segmentation of zebrafish larval fluorescence intensity in specific regions of interest. Quantitative data on the fluorescence intensity and distribution patterns were measured in Quantifish, and advanced statistical and machine learning methods were applied using Orange. Imaging data with eGFP expression results were assessed to evaluate the efficiency of the transgenic protocol. Discussion: This AI-enhanced precision protocol allows for high-throughput screening and quantitative analysis of NFκB reporter transgenesis in zebrafish, enabling the efficient identification and characterization of stable transgenic lines that exhibit tissue-specific expression of the NF-κB reporter, such as lines with induced expression restricted to the retina following LPS stimulation. This approach streamlines the evaluation of regulatory elements, enhances data consistency, and reduces animal use, making it a valuable tool for zebrafish drug discovery. Full article

Thyroid cancer (TC), the most prevalent endocrine neoplasia, has shown a progressive incidence, highlighting the need for new therapeutic approaches—especially for radioiodine-refractory cases, often associated with mutations in genes such as BRAF, RAS, and TP53. This review proposes a mechanistic model that highlights two interrelated characteristics of the tumor microenvironment (TME): redox imbalance and chronic inflammation, key elements in tumor progression and treatment resistance. Thus, natural phenolic compounds, such as curcumin, quercetin, resveratrol, and epigallocatechin gallate (EGCG), function not as simple antioxidants but as pleiotropic agents that reprogram the TME. A central mechanism of action for these compounds is the modulation of the purinergic axis (CD39/CD73/adenosine), a critical immune-metabolic checkpoint. By selectively inducing lethal oxidative stress in tumor cells, suppressing pro-survival inflammatory pathways—such as that mediated by nuclear factor kappa B (NF-κB)—and destabilizing the immunosuppressive shield conferred by adenosine, certain phytochemicals demonstrate the potential to restore immune surveillance and promote tumor apoptosis. In this context, a critical analysis of the evidence related to targeting purinergic signals becomes essential, since pharmacological reinforcement of this pathway, especially when combined with immunotherapies based on immune checkpoint blockade, emerges as a promising strategy for overcoming therapeutic resistance. Full article

Viruses have evolved sophisticated solutions to evade host immunity. One of the most pervasive strategies is molecular mimicry, whereby viruses imitate the molecular and biophysical features of their hosts. This mimicry poses significant challenges for immune recognition, therapeutic targeting, and vaccine development. In this study, we leverage pretrained protein language models (PLMs) to distinguish between viral and human proteins. Our model enables the identification and interpretation of viral proteins that most frequently elude classification. We characterize these by integrating PLMs with explainable models. Our approach achieves state-of-the-art performance with ROC-AUC of 99.7%. The 3.9% of misclassified sequences are signified by viral proteins with low immunogenicity. These errors disproportionately involve human-specific viral families associated with chronic infections and immune evasion, suggesting that both the immune system and machine learning models are confounded by overlapping biophysical signals. By coupling PLMs with explainable AI techniques, our work advances computational virology and offers mechanistic insights into viral immune escape. These findings carry implications for the rational design of vaccines, and improved strategies to counteract viral persistence and pathogenicity. Full article

The global fight against HIV/AIDS has been significantly bolstered by the development and implementation of pre-exposure prophylaxis (PrEP), yet innovation in PrEP interventions, improved adherence and greater access are still needed to maximize its benefit. Nonhuman primate (NHP) infection with simian immunodeficiency virus (SIV) has served as an instrumental animal model in advancing HIV PrEP research. This review comprehensively examines the utility of NHP models in evaluating the efficacy, pharmacokinetics, and safety of diverse PrEP strategies, including oral, injectable, implantable, and topical formulations. It discusses the development of diverse challenge models that simulate human transmission routes and the advantages of NHPs in enabling controlled and mechanistically informative studies. It also highlights the successful translation of pivotal NHP studies evaluating tenofovir-based regimens as well the long-acting agents, cabotegravir and lenacapavir, into the clinical settings, emphasizing the consistently high predictive power of the NHP models for the HIV PrEP clinical efficacy. Finally, it underscores the importance of species-specific pharmacologic considerations and the value of NHP data in informing clinical trial design. As the global community strives to end the HIV epidemic as a public health threat in the absence of an efficacious prophylactic vaccine, NHP models make a critical contribution in the development of next-generation HIV prevention tools. Full article

Background: Influenza A virus (IAV) is a major human pathogen, contributing to substantial morbidity and mortality during seasonal outbreaks and pandemics. Human infection with IAV can lead to pneumonia and acute respiratory distress syndrome (ARDS), and numerous clinical and basic research studies have established an association between IAV and pulmonary fibrosis (PF). However, the treatment of IAV-induced PF fibrosis has not been studied and discussed. Methods: An IAV-induced PF mouse model was established. Herbacetin (HBT) was identified as the most effective compound in the in vitro study of seven components of Rhodiola rosea L. (R. rosea L.). The effect of HBT on IAV-induced lung injury and PF was evaluated in vivo and in vitro. The binding between HBT and neuraminidase (NA) protein was investigated by biological layer interferometry (BLI) and cell thermal shift assay (CETSA). Results: Following IAV infection, the TGF-β/Smad3 pathway is activated, leading to the upregulation of fibrosis-related proteins that promote fibrosis. HBT exhibited a significant ability to reduce influenza virus-induced lung injury and fibrosis both in vitro and in vivo. Mechanistically, HBT binds to the NA protein of the influenza virus, reducing viral infection and the activation of the TGF-β/Smad3 pathway, thereby mitigating the formation of lung injury and PF. Conclusions: HBT represents a promising therapeutic agent for modulating influenza virus-induced lung injury and PF, marking a significant step toward the development of effective treatments for influenza-induced PF. Full article

Despite their disadvantages, preclinical models in vitro are still crucial for every area of biomedical science. They remain a necessary basis for biological, biochemical, and mechanistic studies of pathophysiology of human disease, evaluation of diagnostic tests, assessment of vaccines, as well as screening of potential and repurposed drugs before they are adapted to clinical use. In contrast to animal models in vivo, preclinical in vitro models are cost and time effective. They are easier to use, and, in most cases, they are not associated with ethical concerns. Therefore, they are extensively used in cancer research. Conditional cell reprogramming (CCR) has been one of the novel technologies utilized as a preclinical model in vitro for various common cancers and other diseases. It may be even more important for the research related to rare cancers—elusive, difficult to study, and with insufficient number of relevant models available. Applications of this technology for the basic and translational studies of rare cancers are described in this article. Evaluation of the mechanisms of tumorigenicity and metastasis in neuroblastoma, neuroendocrine cervical carcinoma, ependymoma and astrocytoma, as well as screening of potential drugs and other therapeutic approaches for the laryngeal and hypopharyngeal carcinoma and adenoid cystic carcinoma, demonstrate that the CCR technology is a potential reliable model for various aspects of rare cancer research in the future. Full article

Since its discovery, the BTK inhibitor ibrutinib has redefined the standard treatments for hematological cancers, such as chronic lymphocytic leukemia (CLL). However, concerns exist regarding its secondary effects in humans and its occasional lack of efficacy in certain malignancies. Therefore, combined therapies with ibrutinib have emerged as promising new approaches. In this study, we aimed to explore its therapeutic potential through different approaches. For this purpose, we combined this drug with the BH3 mimetics ABT-199 and ABT-737, which inhibit anti-apoptotic members of the Bcl-2 family, and with the PDK1 inhibitor dichloroacetate (DCA), respectively. As cell models, we used ex vivo samples from patients and also selected the in vitro CLL cell line Mec-1, generating two sub-lines overexpressing Bcl-XL and Mcl-1, a common feature in this cancer. Results demonstrated a synergistic effect for both approaches, in all tumor cells tested, for both cytostatic and cytotoxic effects. Mechanistically, the expression of Bcl-2-family proteins was explored, exhibiting increases in pro-apoptotic, but also in anti-apoptotic, proteins upon ibrutinib treatment and a relative increase in the amount of the pro-apoptotic protein PUMA after treatment with DCA. Our data provides new insights into combined therapies with ibrutinib for CLL, which further expands our knowledge and the potential of this drug for cancer treatment. Full article

Colorectal cancer (CRC) is one of the most common cancers, accounting for approximately 10% of all new cancer cases globally. An increasing number of studies have revealed that the gut microbiome is strongly associated with the pathogenesis and progression of CRC. Based on these advances, this review delineates the mechanistic links between specific microbes and CRC, as well as emerging food-related nutritional intervention strategies. In vivo and in vitro studies have pinpointed the implications of key microbes such as Fusobacterium nucleatum, certain strains of Escherichia coli, enterotoxigenic Bacteroides fragilis, and Enterococcus faecalis, among others, and metabolite involvement and immune responses. Particular attention is paid to the roles of intratumoral microbiota in the development and treatment of CRC, given their direct interaction with tumor cells. Various food-related nutritional intervention strategies have been developed to mitigate CRC risk, including probiotics, antibiotics, or the administration of bioactive compounds such as luteoloside. Finally, we outline critical research directions regarding the influence of animal lineage, carcinoma location, population demographics, the application of advanced in vitro models, and the mediatory roles of gut-associated epithelial cells. In summary, this review might consolidate our current knowledge on the contribution of gut microbiota to CRC and highlights the microbe-based strategies to enhance nutritional interventions for this disease. Full article

Psoriasis is a chronic inflammatory autoimmune skin disease with current treatments often causing significant side effects. This study systematically evaluated the therapeutic potential and mechanisms of polyphenolic compounds in psoriasis treatment. Following PRISMA guidelines, we searched PubMed, Google Scholar, and ScienceDirect databases between January 2008 and September 2023. Studies investigating polyphenolic effects on psoriasis through in vitro, animal, or clinical models were included. Twenty-five studies met inclusion criteria: nine in vitro studies, eleven animal studies, and five clinical trials. Curcumin was most extensively studied, demonstrating 30–60% reductions in inflammatory markers (TNF-alpha, IL-17, IL-22) and significant PASI score improvements. Mechanistic analysis revealed polyphenols primarily target NF-kappaB pathway inhibition and IL-17/Th17 axis suppression, addressing fundamental inflammatory processes in psoriatic pathophysiology. However, limited clinical evidence represents a significant implementation barrier. Polyphenols show potential as adjunctive therapies to conventional topical and systemic treatments. Future research should prioritize large-scale randomized controlled trials with standardized formulations and combination therapy investigations to establish clinical efficacy and overcome bioavailability challenges. Full article

Protactinium-231 (²³¹Pa), a particle-reactive radionuclide derived from ²³⁵U decay, serves as a pivotal tracer in marine geochemistry and paleoceanography, offering unique insights into particle scavenging, deep ocean circulation, and sedimentary processes. This review synthesizes significant advances in ²³¹Pa research. A core application lies in utilizing the ²³¹Pa/²³⁰Th ratio as a sensitive proxy for reconstructing past Atlantic Meridional Overturning Circulation (AMOC) intensity, with compelling evidence indicating a substantially weakened AMOC during the Last Glacial Maximum compared to the Holocene. Major technological breakthroughs, particularly the advent of high-precision ICP-MS and TIMS methodologies, have revolutionized the quantification of ²³¹Pa in both dissolved and particulate phases, enabling spatial and temporal resolution. Looking forward, the integration of high-resolution sediment core analyses—featuring refined ²³¹Pa/²³⁰Th chronologies—with advanced climate models offers a powerful pathway to significantly enhance our mechanistic understanding of the ocean’s role in global climate regulation. This synergistic approach will help constrain the dynamics of oceanic overturning circulation and its critical functions in carbon sequestration and heat redistribution across past, present, and future climate scenarios. Full article

APOBEC3B (A3B) has been implicated in host–virus interactions, but its role in SARS-CoV-2 infection is unclear. Here, we demonstrate that A3B is overexpressed in bronchoalveolar lavage fluid (BALF) cells from severe COVID-19 patients compared to those with mild disease. A3B knockdown in Caco-2 cells significantly reduces SARS-CoV-2 infectivity, likely through attenuation of the PKR-mediated integrated stress response, a pathway proposed to promote SARS-CoV-2. Single-cell RNA sequencing (scRNA-seq) data suggest that BALF cells from severe COVID-19 patients exhibit a repressed state for cellular translation, potentially mediated by eIF2α phosphorylation. However, in A549-ACE2 cells, SARS-CoV-2 does not activate PKR, but A3B knockdown still reduces SARS-CoV-2 infectivity, suggesting an alternative mechanism of action in different cellular contexts. To further investigate A3B’s role in severe COVID-19, we employed Geneformer, a transformer-based machine learning model, which predicted that A3B knockout would perturb AMPD2 (adenosine monophosphate deaminase 2), a key enzyme in purine metabolism and immune regulation. We validated this prediction using bulk RNA-seq and clinical scRNA-seq data, confirming that AMPD2 expression is downregulated in severe COVID-19 but restored upon A3B knockdown. Together, these findings suggest that A3B plays a proviral role in SARS-CoV-2 infection by modulating translational control and immune regulatory networks, warranting further studies to elucidate the underlying mechanistic details. Full article

Background: Helicobacter pylori (H. pylori) is a major pathogen associated with a variety of gastrointestinal disorders, including gastritis, peptic ulcers, and gastric cancer. As a natural bioactive product, propolis exhibits multifaceted and multi-mechanistic effects. Due to its immunomodulatory, anti-inflammatory, and antioxidant properties, propolis has emerged as a promising therapeutic alternative, offering an innovative approach to managing H. pylori infections and providing new insights into addressing antibiotic resistance. Methods: This comprehensive review, synthesizing data from PubMed, ScienceDirect, and SciFinder, examines the mechanisms by which propolis combats H. pylori. Results: Propolis has demonstrated significant antibacterial efficacy against H. pylori in both in vitro and in vivo models. Its multitargeted mechanisms of action include direct inhibition of bacterial growth, interference with the expression of virulence factors, suppression of virulence-associated enzymes and toxin activity, immunomodulation, and anti-inflammatory effects. These combined actions alleviate gastric mucosal inflammation and damage, reduce bacterial colonization, and promote mucosal healing through antioxidant and repair-promoting effects. Furthermore, propolis disrupts oral biofilms, restores the balance of the oral microbiome, and exerts bactericidal effects in the oral cavity. Synergistic interactions between propolis and conventional medications or other natural agents highlight its potential as an adjunctive therapy. Conclusions: Propolis demonstrates dual functionality by inhibiting the release of inflammatory mediators and suppressing H. pylori growth, highlighting its potential as an adjuvant therapeutic agent. However, clinical translation requires standardized quality control and higher-level clinical evidence. Future research should focus on validating its clinical efficacy and determining optimal dosing regimens, and exploring its role in reducing H. pylori recurrence. Full article

Background: Post-myocardial infarction (MI) heart failure (HF) is characterized by myocardial energy metabolism disorder, with excessive glycolysis playing a key role in its progression. Silybin (SIL), a flavonoid derived from Silybum marianum, has demonstrated hepatoprotective and metabolic regulatory effects. However, the role of this flavonoid in ameliorating post-myocardial infarction heart failure (post-MI HF) by modulating energy metabolism remains unclear. Methods: This study employed an oxygen–glucose deprivation (OGD) model to induce myocardial cell injury in vitro, with YC-1 treatment used to inhibit hypoxia-inducible factor-1α (HIF-1α) for mechanistic validation. A myocardial infarction-induced HF mouse model was used for in vivo experiments. Results: In vitro, SIL enhanced cell viability, increased ATP levels, and decreased lactate production and reactive oxygen species (ROS) accumulation in OGD-treated myocardial cells. SIL downregulated the mRNA and protein expression of HIF-1α, 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3), glucose transporter 1 (GLUT1), and lactate dehydrogenase A (LDHA) while inhibiting HIF-1α nuclear translocation. Furthermore, SIL suppressed glycolytic proteins (PFKFB3, GLUT1, and LDHA) in a manner comparable to the HIF-1α inhibitor YC-1. This confirms that SIL’s inhibition of glycolysis is HIF-1α-dependent. In vivo, SIL treatment improved cardiac function parameters (LVEF and LVFS) and attenuated left ventricular remodeling (LVID;d and LVID;s) in post-MI HF mice. Additionally, myocardial fibrosis markers were significantly reduced, accompanied by a decrease in the myocardial mRNA and protein expression of glycolytic proteins, including HIF-1α, PFKFB3, GLUT1, and LDHA. Conclusions: Silybin effectively ameliorates post-myocardial infarction heart failure through the HIF-1α-mediated regulation of glycolysis, leading to improved myocardial energy metabolism and enhanced cardiac function. Full article