Search Results (30,947)

At present, there is still a lack of effective treatments to slow the progression of Parkinson’s disease. Naturally derived active substances, valued for their safety and multi-target potential, have become an important direction in anti-PD drug development, with marine organisms representing a valuable source of bioactive peptides. This study aimed to isolate and identify anti-PD peptides from Rapana venosa protein hydrolysates. Through bioactivity-guided screening combined with an MPTP-induced zebrafish PD model, three novel active peptides—KSTELLI, FLVKLPMFM, and SDSLSEILIS—were successfully identified. The study showed that these peptides significantly alleviated dopaminergic neuron loss, improved the cerebral vascular system, restored motor and sensory function, and alleviated oxidative stress. Molecular docking confirmed their stable binding to key PD targets (DDC, α-synuclein, and MAO-B). Further transcriptomic and gene expression analyses revealed that their neuroprotective effects involve the regulation of pathways related to metabolism, oxidative stress, inflammation, and apoptosis, with the three peptides exhibiting distinct mechanistic emphases. The research demonstrates that these marine-derived peptides exert neuroprotective effects through a synergistic multi-target mechanism, laying a foundation for the development of novel lead compounds against Parkinson’s disease. Full article

Tumor cell heterogeneity and multicellular interactions critically influence drug resistance, recurrence, and prognosis. Here, CPcellsubpopulation, a computational framework integrating scRNA-seq, bulk RNA-seq, and clinical data was developed to identify cancer progression-associated cell subpopulations. Then, the integrated analyses of scRNA-seq and spatial transcriptomics were performed to predict potential interactions, identify critical transcription factors, and predict candidate anticancer drugs. Across nine cancers, we detected cancer progression-associated cell subpopulations significantly linked to prognosis, with consistent patterns across cancer types. In renal cell carcinoma (RCC), we identified conserved metabolic^high UBE2C+ cancer cells linked to poor outcomes, metabolic reprogramming and low differentiation, and PLK1+ NK cells, plasma cells, and CDC20+ macrophages associated with advanced stages and unfavorable prognosis. Spatial mapping revealed spatial association of RCC progression-associated cancer and immune cell subpopulations, suggesting the potential role of the VEGF, GDF, PTN and IL16 pathways in the remodeling of the tumor microenvironment. Gene regulatory network analysis highlighted RAD21 as a key regulator linking metabolism and therapy resistance. This study provides a systematic pipeline to delineate cancer progression-associated cell subpopulations, uncovers metabolic^high UBE2C+ cancer cells as progression-associated tumor cell population, and nominates critical regulators and compounds as therapeutic targets. Full article

Ascosphaera apis, an obligate lethal fungal pathogen that infects bee larvae, and causes chalkbrood disease, poses a significant threat to the global beekeeping industry. Long non-coding RNAs (lncRNAs) are employed by pathogens to enhance infectivity and evade host immunity. Here, lncRNAs in A. apis spores (AaCK group) and the guts of 4-, 5-, and 6-day-old Apis cerana cerana worker larvae inoculated with A. apis spores (AaT1, AaT2, and AaT3 groups) were identified, characterized, and validated. Additionally, the expression pattern of fungal lncRNAs during infection was analyzed, followed by an investigation of the regulatory manners and roles of differentially expressed lncRNAs (DElncRNAs). A total of 1379 lncRNAs were identified in AaCK, AaT1, AaT2, and AaT3 groups using bioinformatics, involving various types such as sense lncRNAs, antisense lncRNAs, bidirectional lncRNAs, intergenic lncRNAs, and intronic lncRNAs. Additionally, 4, 9, and 75 up-regulated lncRNAs as well as 2, 1, and 15 down-regulated ones were identified in the 4-, 5-, and 6-day-old larval guts following A. apis inoculation. Fifteen DElncRNAs as potential antisense lncRNAs may interact with 15 sense-strand mRNAs in the AaCK vs. AaT3 comparison group. Cis-acting analysis identified 10, 16, and 136 upstream and downstream genes of DElncRNAs in the aforementioned comparison groups, involving a series of GO terms and KEGG pathways like metabolic process and biosynthesis of secondary metabolites. Following the trans-acting investigation, 752, 821, and 1327 co-transcribed genes with DElncRNAs were discovered, spanning an array of functional terms and pathways such as biological processes and glycerophospholipid metabolism. Analysis of a competing endogenous RNA (ceRNA) network indicated that 1 and 5 DElncRNAs in the AaCK vs. AaT1 and AaCK vs. AaT3 comparison groups potentially targeted 1 and 2 miRNAs, further targeting 208 and 286 mRNAs, respectively. Further analysis identified one ceRNA axis relevant to the MAPK signaling pathway and several ceRNA networks associated with the biosynthesis of secondary metabolites. Finally, RT-qPCR results confirmed that the expression trends of six randomly selected DElncRNAs were consistent with those in the transcriptome data. These findings not only offer a foundation for elucidating the mechanisms underlying DElncRNA-mediated A. apis infection but also enrich our understanding of honeybee host–fungal pathogen interactions. Full article

Restless legs syndrome (RLS) is a common sensorimotor disorder with limited treatment options and incompletely understood pathophysiology. Genome-wide association studies have identified numerous risk loci, but translating these findings into causal genes and therapeutic targets remains challenging. We performed a proteome-wide association study (PWAS) integrating RLS genome-wide association study (GWAS) data from FinnGen with two brain pQTL datasets (ROSMAP and Banner). We validated the identified proteins using TWAS, SMR, and colocalization analyses using brain pQTL and eQTL datasets. To further investigate peripheral protein associations, we performed SMR using plasma pQTL data from the UK Biobank Pharma Proteomics Project (UKB-PPP). We also conducted a phenome-wide association study (PheWAS) to screen for potential off-target effects of the prioritized genes, followed by drug prediction using DSigDB and molecular docking. PWAS identified GLO1, along with GRWD1 and MAP2K5, as significantly associated with RLS. GLO1 was identified by brain-based SMR (p = 0.0001), colocalization (PP.H4 = 0.96), TWAS (p = 0.048), and was confirmed by plasma-based SMR (p = 3.16 × 10⁻⁹) as the only protein associated with RLS. PheWAS analysis, without associations for 783 non-RLS phenotypes, confirmed the specificity of GLO1. Among 27 predicted GLO1-targeting compounds, Gambierol had the strongest binding affinity (−8.3 kcal/mol). This proteogenomic study identifies GLO1 as a prioritized causal gene and promising drug target for RLS, combining brain and plasma data to provide new insights into pathogenesis and candidate drug development. Full article

Prostate adenocarcinoma (PRAD) poses a significant challenge due to therapy resistance and an immunosuppressive tumor microenvironment (TME). Ferroptosis has emerged as a therapeutic vulnerability, yet its immunomodulatory role in PRAD remains elusive. Here, we employed a multi-omics approach—integrating bulk RNA-seq (498 tumors), single-cell RNA-seq (68,322 cells), and spatial transcriptomics (19,483 spots)—to decode the ferroptosis-immune landscape. We derived a robust 16-gene ferroptosis signature that predicted biochemical recurrence (C-index = 0.76) and validated it in two independent cohorts. Crucially, high-risk tumors exhibited a “cold” immunosuppressive TME enriched in regulatory T cells and M2 macrophages, alongside elevated immune checkpoints (HAVCR2, CTLA4, PDCD1). Single-cell and virtual knockout analyses revealed that cancer epithelial cells evade ferroptosis via NFE2L2-associated antioxidant defenses, which strongly correlates with immune exclusion. Spatial transcriptomics further demonstrated spatially organized vulnerabilities, with ferroptosis-resistant tumor cores and immune-infiltrated invasive margins. To identify therapeutic interventions, we utilized drug response modeling and molecular docking, prioritizing RSL3, Atovaquone (targeting NOX4 (NADPH oxidase 4)/DHODH), and Sorafenib (targeting TrxR1 (thioredoxin reductase 1, encoded by TXNRD1)) as potent agents with potential ferroptosis-modulatory activity. Collectively, our findings demonstrate that NFE2L2-associated ferroptosis resistance shapes immune evasion in PRAD. Targeting ferroptosis regulators provides a compelling therapeutic rationale to remodel the TME and synergize with immune checkpoint blockade. Full article

Background/Objectives: Liuwei Dihuang (LWDH) is a classical plant-derived herbal formula widely used for cognitive decline. This study aimed to evaluate its efficacy and safety in cognitive disorders and to explore its potential pharmacological mechanisms using network pharmacology. Methods: We searched 11 databases through November 2024 for randomized controlled trials comparing LWDH plus conventional therapy with conventional therapy alone in cognitive disorders. Meta-analysis was performed for clinical outcomes, and herb–compound–target and disease-target datasets were integrated to identify core molecular modules. Results: Twelve randomized controlled trials involving 1137 participants were included. Adjunctive LWDH was associated with improvements in Mini-Mental State Examination scores (MD = 2.34, 95% CI 0.88–3.79), activities of daily living, and quality of life. However, substantial heterogeneity and methodological limitations, including unclear randomization and blinding, were observed across studies, indicating a potential risk of bias. Fewer adverse events were reported in the LWDH plus conventional treatment group, although reporting quality was limited. The overall risk of bias was judged as “some concerns”. Network pharmacology analysis identified a broad set of overlapping genes between LWDH-associated targets and cognitive disorder-related genes, which were further refined through filtering procedures. Subsequent analyses suggested associations with pathways related to neurodegeneration, apoptosis, and central nervous system function; however, these findings are exploratory and based on in silico predictions. Conclusions: LWDH may be associated with potential adjunctive benefits in cognitive disorders. However, given the methodological limitations and clinical heterogeneity of the included studies, the findings should be interpreted with caution. The proposed pharmacological mechanisms are exploratory and require further validation. Well-designed randomized controlled trials are needed to establish more robust evidence. Full article

Ultraviolet radiation (UVR) exposure accelerates skin aging by disrupting cellular homeostasis and inducing epigenetic changes, such as promoter hypermethylation of key regulatory genes. However, the molecular mechanisms underlying UVR-driven epigenetic silencing remain poorly understood. By integrating high-throughput DNA methylation profiling with co-regulatory network analysis, we identified KIT as a hub gene in a photoaging-associated methylation module. Pathway enrichment further revealed coordinated hypermethylation of the canonical Wnt/β-catenin signaling pathway, establishing the Wnt/KIT axis as a critical epigenetic-signaling nexus in UVR-induced skin fibroblast aging. In immortalized human skin fibroblasts (HSFs), UVR suppressed Wnt signaling, leading to KIT promoter hypermethylation, transcriptional silencing, and premature photoaging. Gain-of-function studies revealed that reversing KIT hypermethylation either via Wnt pathway activation or KIT overexpression effectively mitigated photoaging-associated phenotypes. Crucially, we found that puerarin (PUE), a natural isoflavone, reversed UVR-induced epigenetic silencing by directly interacting with β-catenin, reactivating Wnt signaling, and restoring KIT expression. PUE treatment preserved cellular function in UVR-damaged fibroblasts. These findings establish the Wnt/β-catenin-KIT axis as a critical epigenetic driver of skin aging and highlight puerarin as a promising therapeutic candidate for targeted anti-aging intervention. Full article

Generalized pustular psoriasis (GPP) is a rare, severe, and potentially life-threatening inflammatory dermatosis increasingly recognized as a distinct disease entity rather than a variant of plaque psoriasis. Emerging evidence indicates that GPP is primarily driven by dysregulation of the interleukin-36 (IL-36) signaling axis, leading to amplification of proinflammatory cascades in keratinocytes and a predominantly innate, neutrophil-driven immune response. This promotes rapid neutrophil recruitment, sterile pustule formation, and abrupt cutaneous and systemic inflammation. Consistent with this, GPP demonstrates a greater predominance of innate immune and neutrophil-driven inflammation, whereas plaque psoriasis is more strongly associated with IL-23/Th17-mediated adaptive immune responses. Transcriptomic and genetic studies further support this distinction, demonstrating enrichment of IL-36-associated and neutrophil-related signatures, activation of MyD88-dependent pathways, and mutations in genes regulating the IL-36 axis, including IL36RN, AP1S3, and CARD14. Consequently, conventional systemic therapies and biologics targeting TNF-α, IL-17, and IL-23 pathways show variable efficacy and may act more slowly in GPP. In contrast, IL-36 receptor inhibitors represent a more mechanism-aligned approach and have demonstrated rapid and clinically meaningful responses in acute flares. However, important gaps remain, including the lack of validated biomarkers and limited data on long-term treatment outcomes. This review provides an integrated perspective on IL-36-driven inflammation in GPP, including comparison with plaque psoriasis, and outlines its implications for mechanism-based therapeutic approaches. Full article

The increasing volume of plant-based waste generated by the agri-food sector represents both an environmental challenge and an underexploited biotechnological resource. These wastes, rich in lignocellulosic compounds, constitute a natural habitat for specialized microorganisms. The aim of this article is to provide a critical review of the potential use of such wastes—specifically straw, pomace, and manure—in two complementary ways: (1) as a specific source for isolating new microbial strains with high biodegradation capacity and plant-growth-promoting potential, and (2) as a low-cost substrate for their propagation, e.g., in solid-state fermentation processes. This dual perspective represents a novel, integrative approach, as previous reviews typically address these aspects in isolation rather than considering their synergistic potential. The article discusses the relationship between the chemical composition of selected wastes (straw, pomace, manure) and the targeted selection of desirable microbiological traits. Particular emphasis is placed on advanced, integrated approaches for assessing microbial potential, combining phenotyping (zymography, activity assays), genomics (whole-genome sequencing—WGS, identification of CAZyme genes and biosynthetic gene clusters), and metabolomics (metabolite profiling, 3D MSI imaging). The limitations of individual methods are critically evaluated, and key research gaps are identified, including the need for in situ validation of omics-based findings and the development of stable microbial consortia with predictable performance under variable environmental conditions. These gaps are discussed in the broader context of circular bioeconomy and sustainable agriculture, highlighting the strategic relevance of integrating waste valorization with microbiome-based biotechnological innovations. Full article

Background: Age-related macular degeneration (AMD) is a common retinal degenerative disease linked to adaptive immune response dysregulation. This study aimed to identify shared immune-related biomarkers and explore their underlying mechanisms. Methods: GSE29801 and GSE135092 served as training and validation sets. Adaptive immune response-related genes (AIR-RGs) from MSigDB were intersected with AMD-related differentially expressed genes (DEGs) to identify candidate genes. Machine learning algorithms were applied to screen biomarkers, validated in datasets and a mouse model of choroidal neovascularization by qPCR. A nomogram was constructed and assessed. GSEA and immune infiltration analyses explored mechanisms and immune microenvironment associations. Results: A total of 148 DEGs were identified, yielding 15 candidate genes after intersection with AIR-RGs. Machine learning identified C3 and HLA-DOA as potential biomarkers, with their differential expression validated across datasets. A nomogram based on these biomarkers demonstrated good predictive performance for AMD pathology (AUC = 0.795). Biomarkers were associated with some immune-inflammatory pathways. Significant differences in immune cell infiltration were observed between AMD and control groups, with biomarkers positively correlated with differentially infiltrated immune cells, such as natural killer cells. Conclusions: The identification of the established biomarker C3 serves as a proof-of-principle for the analytical approach, rather than a novel discovery, thereby validating the model’s capacity to uncover other critical immune targets. Consequently, C3 and HLA-DOA serve as potential biomarkers for AMD, significantly correlated with disease progression via immune pathways and offering insights for immune-based therapeutic strategies. Full article

Acute kidney injury (AKI) lacks targeted pharmacological interventions. While the DanShen–DaHuang (DS-DH) herb pair shows clinical potential for AKI treatment, and our prior study has validated its nephroprotective efficacy in a cisplatin-induced murine model, its specific molecular targets within the renal microenvironment remain undefined. In this study, we integrated network pharmacology and weighted gene co-expression network analysis (WGCNA) to screen AKI-related targets of the DS-DH pair. A multi-algorithmic machine learning pipeline (including LASSO, Boruta, Random Forest, GBM, XGBoost, and Decision Trees) was utilized to calculate feature importance scores and rank core genes. Subsequently, single-cell RNA sequencing (scRNA-seq) data (GSE197266) were analyzed for transcriptomic mapping, pseudotime trajectory, and cell–cell communication. Finally, molecular docking evaluated theoretical binding affinities. After database screening, a total of 603 drug–disease intersecting targets were obtained. Subsequently, 917 module genes significantly associated with AKI were identified by WGCNA, and 62 core candidate genes were determined after intersecting with the above targets. Multi-algorithm machine learning ranked the importance of the 62 targets, with transketolase (TKT) ranking the highest. To elucidate the mechanism of TKT in AKI, scRNA-seq analysis was performed on 77,593 high-quality cells. The results showed that Tkt was specifically enriched in renal macrophages, with the highest expression in the M2-polarized subset. Pseudotime analysis further revealed that Tkt expression dynamics were highly synchronized with the differentiation trajectory of M2 macrophages and positively correlated with the repair markers Arg1 and Mrc1. Cell–cell communication analysis predicted that Tkt⁺ M2 macrophages act as active communication hubs via the Spp1 and Mif signaling axes. Molecular docking validated the favorable binding affinity between core DS-DH compounds and the TKT active pocket. This computational framework predicts that the DS-DH herb pair might mitigate AKI by potentially targeting TKT, a metabolic enzyme closely associated with macrophage M2 polarization. By prioritizing targets via multi-algorithmic scoring, we provide a data-driven rationale and candidate targets for future experimental validation. Full article

Grain number is a primary agronomic trait for targeted yield improvement, with the prospect of enhanced grain production leading to greater food security. Given the complex polygenic nature of the grain number trait, large sample sizes are essential for effective QTL identification. The implementation of trained computer vision models for grain detection offers a timely and cost-effective solution for rapid QTL isolation. In this study, we trained a grain detection model using Ultralytics’ You Only Look Once (YOLOv11) framework. Training was completed on 1000 images of barley spikes, derived from a doubled haploid (DH) population descended from Hindmarsh and RGT Planet. The trained model, termed BarleyGC, achieved satisfactory accuracy metrics (mAP50-95 = 71.9%, recall = 96.7%, precision = 97.1%). Phenotypic characterisation of the DH population was completed with BarleyGC on a distinct collection of 973 images. The Pearson correlation coefficient (r) between model and manual-derived counts for the trait of grain number per spike was 0.895 (p < 0.0001), and 92.4% of all measurements fell within three grains of the manual measurement. Downstream QTL analysis on the phenotype data (n = 153 DH lines), revealed a QTL peak at position 224.959 cM on the genetic map (LOD = 3.14), named qGN-2H. The QTL region contained 20 candidate genes—including HORVU2Hr1G092290 (HORVU.MOREX.r3.2HG0184740), encoding the six-rowed spike 1 (Vrs1) gene—a well-characterised major regulator of row-type divergence and lateral spikelet development. Our study demonstrates the power of the YOLOv11 framework for grain quantification, with BarleyGC capable of grain detection directly from images of in-tact spikes in two-rowed barley varieties—thus achieving accelerated sample processing for the grain number trait. Full article

Epimedium is a traditional Chinese tonic used to tonify the kidneys, enhance sexual function, and strengthen muscles and bones. However, the potential effects of Epimedium on the semen quality of Bama boars remain incompletely elucidated. The objective of this study was to evaluate the effects of dietary Epimedium ultrafine powder (EP) supplementation on the semen quality of Bama boars and to explore the underlying mechanisms. The objective of this study was to evaluate the effects of dietary EP supplementation on the semen quality of Bama boars and to explore the underlying mechanisms. Eighteen healthy, sexually mature adult male Bama boars were randomly divided into three groups (n = 6) and fed either a basal diet (CON) or the basal diet supplemented with 0.3% (EP3) or 0.5% (EP5) Epimedium ultrafine powder for five weeks. This study employed enzyme-linked immunosorbent assay (ELISA), 16S RNA gene sequencing, non-targeted metabolomics (CON and EP5), and Spearman correlation analysis, among other methods. The results indicated that dietary Epimedium (0.3% and 0.5%) increased the levels of serum TP, FSH, and SOD and decreased the abnormal sperm rate and the levels of serum TBA, TNF-α, and IL-6. Among them, adding 0.5% Epimedium in the diet increased sperm motility and the levels of serum T, LH, and IgG. 16S rRNA gene sequencing analysis revealed that both 0.3% and 0.5% Epimedium supplementation reduced the abundance of Streptococcus. Specifically, the 0.3% dose decreased Prevotella abundance, while the 0.5% dose reduced Escherichia-Shigella abundance. PICRUSt2 analysis revealed that the pathways of phenylalanine, butanoate, biotin, and arachidonic acid metabolism were significantly enriched in the Epimedium group. A non-targeted metabolomics analysis identified that indole-3-acrylic acid, DL-tryptophan, 2-hydroxyphenylalanine, and propionylcarnitine showed significant upregulation after Epimedium supplementation. Spearman correlation analysis indicated that Streptococcus was negatively correlated with sperm motility and serum-related parameters (TP, T, LH, IgM, and IgG). Streptococcus and Escherichia-Shigella were negatively correlated with indole-3-acrylic acid, DL-tryptophan, and biotin. In conclusion, Epimedium has a positive impact on the seminal quality, reproductive hormones, and immune–antioxidant levels of Bama boars by regulating the composition and metabolites of the intestinal microbiota. Full article

Moyamoya angiopathy (MMA) is a rare, chronic progressive cerebrovascular condition characterized by bilateral stenosis or occlusion of the terminal internal carotid arteries and their major branches. This progressive occlusion triggers the development of telangiectatic and fragile vessels at the base of the brain, creating the characteristic angiographic appearance of a “puff of smoke.” Depending on the etiology, MMA is classified as Moyamoya Disease (MMD) when idiopathic and primary or Moyamoya Syndrome (MMS) when associated with underlying systemic conditions. While the RNF213 gene, particularly the p.R4810K variant, is recognized as the major susceptibility locus for MMD in East Asian populations, it does not fully account for the global genetic landscape or the phenotypic diversity of the disease. This review provides a comprehensive overview of the genetic architecture of the entire MMA spectrum, exploring loci beyond RNF213. We analyze the role of genes involved in vascular smooth muscle cell contractility (ACTA2, MYH11), TGF-β signaling, and DNA repair mechanisms that drive MMS, alongside the genetic basis of syndromic forms associated with neurofibromatosis type 1, trisomy 21, and RASopathies. Understanding these diverse genetic drivers is crucial for early diagnosis, risk stratification, and the development of targeted molecular therapies. Full article

Background: Neuroinflammation is increasingly recognized as a central mechanism in the pathogenesis of epilepsy, particularly drug-resistant epilepsy (DRE), where conventional anti-seizure medications fail to achieve adequate control. Microglia, the resident immune cells of the central nervous system, play a critical role in mediating inflammatory responses that contribute to seizure initiation, propagation, and pharmacoresistance. Persistent microglial activation promotes the release of pro-inflammatory mediators, exacerbating neuronal hyperexcitability and epileptogenesis. Objectives: This scoping review aimed to systematically map the existing evidence on microglial activation in DRE and to identify emerging therapeutic strategies targeting microglia-mediated neuroinflammation. Methods: The review was conducted in accordance with Joanna Briggs Institute (JBI) methodology and reported following PRISMA-ScR guidelines. A comprehensive search of PubMed, PubMed Central, Scopus, Google Scholar, Embase, and Web of Science was performed without date restrictions. Eligible studies included preclinical, clinical, and review articles investigating microglial activation, neuroinflammatory pathways, or microglia-targeted therapies in epilepsy. Data were charted and synthesized using a narrative approach. Results: A total of 521 records were identified, of which 53 studies met the inclusion criteria after screening and full-text review. The included studies, published between 1998 and 2021, demonstrated a growing research interest in microglia-related mechanisms in epilepsy. Evidence consistently highlighted the role of microglial activation in promoting neuroinflammation and seizure persistence. Emerging therapeutic strategies included anti-inflammatory pharmacotherapies, microglial modulators, cannabinoid-based interventions, gene therapy, and stem cell-based approaches. Conclusions: Targeting microglial activation represents a promising and evolving therapeutic strategy for DRE. While preclinical and early clinical evidence is encouraging, challenges related to specificity, timing, and translational applicability remain. Future research should focus on precision-based interventions to optimize clinical outcomes and enable disease modification beyond seizure control. Full article