Biology-Basel最新文献

{"title":"Exploring the Molluscan Microbiome: Diversity, Function, and Ecological Implications.","authors":"Tsireledzo Goodwill Makwarela, Nimmi Seoraj-Pillai, Tshifhiwa Constance Nangammbi","doi":"10.3390/biology14081086","DOIUrl":"10.3390/biology14081086","url":null,"abstract":"<p><p>Mollusks are among the most ecologically and economically significant invertebrates; yet, their associated microbiomes remain understudied relative to those of other metazoans. This scoping review synthesizes the current literature on the diversity, composition, functional roles, and ecological implications of molluscan microbiomes, with an emphasis on three major groups: gastropods, bivalves, and cephalopods. Drawing on studies from terrestrial, freshwater, and marine systems, we identified the dominant bacterial phyla, including Proteobacteria, Bacteroidetes, and Firmicutes, and explored how microbiota vary across different habitats, diets, tissue types, and host taxonomies. We examined the contribution of molluscan microbiomes to host functions, including digestion, immune modulation, stress responses, and nutrient cycling. Particular attention was given to the role of microbiota in shell formation, pollutant degradation, and adaptation to environmental stressors. The review also evaluated microbial interactions at different developmental stages and under aquaculture conditions. Factors influencing microbiome assembly, such as the host's genetics, life history traits, and environmental exposure, were mapped using conceptual and graphical tools. Applications of molluscan microbiome research in aquaculture, conservation biology, and environmental biomonitoring are highlighted. However, inconsistencies in the sampling methods, taxonomic focus, and functional annotations limit the generalizability across taxa. We identify key knowledge gaps and propose future directions, including the use of meta-omics, standardized protocols, and experimental validation to deepen insights. By synthesizing emerging findings, this review contributes to a growing framework for understanding mollusk-microbiome interactions and their relevance to host fitness and ecosystem health. It further establishes the importance of mollusks as model systems for advancing microbiome science.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12383823/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144993766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing Pollinator Support: Plant-Pollinator Dynamics Between <i>Salvia yangii</i> and <i>Anthidium</i> Bees in Anthropogenic Landscapes.","authors":"Daniela Lupi, Claudia Giuliani, Gelsomina Fico, Serena Malabusini, Carla Sorvillo, Manuela Giovanetti","doi":"10.3390/biology14081084","DOIUrl":"10.3390/biology14081084","url":null,"abstract":"<p><p>Anthropogenic environments are increasingly recognised for their potential to support pollinator diversity, especially through the strategic selection of ornamental plant species. This study investigated the ecological role of <i>Salvia yangii</i> (formerly <i>Perovskia atriplicifolia</i>) in supporting solitary bees, particularly species of the genus <i>Anthidium</i>, within urban green spaces in Milan (Italy). Field observations were conducted in both urban and rural sites to assess pollinator visitation rates, bee abundance, and plant traits relevant to nesting and foraging. <i>S. yangii</i> attracted a diverse assemblage of bee genera, with <i>Anthidium</i> spp. consistently recorded as dominant visitors. This preference is likely driven by the short corolla tube, which facilitates the access to nectar, and its dense coverage of trichomes, which may serve as essential nesting materials. The interaction was found to be stable across environments, suggesting that <i>S. yangii</i> provides reliable floral and structural resources. These findings highlight the potential of specific ornamental plants to contribute meaningfully to urban pollinator conservation. While the use of exotic species warrants caution, we propose that <i>S. yangii</i> may be suitable for inclusion in pollinator-friendly planting guidelines under controlled horticultural conditions, offering a promising model for enhancing urban biodiversity through informed plant selection.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12383519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taurine Supplementation Enhances the Resistance of <i>Litopenaeus vannamei</i> Postlarvae to Low-Salinity Stress.","authors":"Huaichi Wang, Xinyue Du, Jiahong Zou, Mengya Wang, Yan Lei, Bin Zhang, Yongzhen Zhao, Linyuan Jiang, Xiaohan Chen, Qingchao Wang","doi":"10.3390/biology14081082","DOIUrl":"10.3390/biology14081082","url":null,"abstract":"<p><p>In aquaculture, Pacific white shrimp (<i>Litopenaeus vannamei</i>) growth in low-salinity waters is limited by osmoregulatory stress; therefore, improving resistance to low-salinity stress via nutritional modulation is key. In the present study, shrimp postlarvae were provided with a taurine supplement under low-salinity stress, and then the survival rate, the histology, the Na⁺/K⁺-ATPase (NKA) expression pattern and transcriptomic sequencing were investigated to evaluate the postlarval responses. The results showed that the postlarva survival rate in low-salinity water was only 61.11%, which is significantly lower than that for postlarvae reared in saline water (92.67%). However, taurine supplementation significantly increased the postlarva survival rate in low-salinity culture to 76.67% and also increased the shrimp body length. Moreover, immunofluorescence and enzyme activity assays indicated that taurine alleviated NKA overactivation in the shrimp postlarvae under low-salinity stress. Furthermore, a GO enrichment analysis of differentially expressed genes suggested that the overactivation of hormone and receptor signaling under low-salinity stress was significantly downregulated after taurine supplementation. On the other hand, taurine supplementation may promote epithelial cell proliferation in shrimp postlarvae by negatively regulating the Wnt signaling pathway. These findings suggest that taurine may enhance the shrimp postlarval osmoregulatory capacity, thereby improving their ability to acclimatize to low-salinity environments.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12383651/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144993977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Harnessing the Power of Microbiota: How Do Key <i>Lactobacillus</i> Species Aid in Clearing High-Risk Human Papilloma Virus Infection and Promoting the Regression of Cervical Dysplasia?","authors":"Edyta Kęczkowska, Joanna Wrotyńska-Barczyńska, Aneta Bałabas, Magdalena Piątkowska, Michalina Dąbrowska, Paweł Czarnowski, Ewa E Hennig, Maciej Brązert, Piotr Olcha, Michał Ciebiera, Natalia Zeber-Lubecka","doi":"10.3390/biology14081081","DOIUrl":"10.3390/biology14081081","url":null,"abstract":"<p><p><i>Lactobacillus</i> species play a fundamental role in maintaining a healthy vaginal microbiota and have been increasingly recognized for their protective effects against high-risk human papillomavirus (HR-HPV) infection and the progression of cervical intraepithelial neoplasia (CIN). These beneficial bacteria contribute to host defense through multiple mechanisms, including the production of lactic acid that sustains a low vaginal pH, enhancement of epithelial barrier integrity via E-cadherin regulation, and modulation of immune signaling pathways such as interferon responses and NF-κB activity. <i>Lactobacillus</i> strains exert anti-inflammatory effects by downregulating pro-inflammatory cytokines and interfering with oncogenic pathways including Wnt/β-catenin and the expression of HPV E6 and E7 proteins. Additionally, they may regulate tumor-suppressor microRNAs and modulate dendritic cell and macrophage activity, supporting antiviral immunity. Recent studies have explored their potential influence on CIN regression and HR-HPV clearance, particularly the strains <i>Lactobacillus crispatus</i> and <i>L. gasseri</i>, which are associated with favorable microbial community states. This review explores the potential mechanisms through which <i>Lactobacillus</i> species contribute to HR-HPV clearance and the regression of cervical dysplasia, integrating evidence from molecular studies, in vivo models, and clinical trials. The emerging role of probiotic interventions as adjunctive strategies in HPV management is also discussed, highlighting their possible synergy with conventional treatments and prophylactic vaccination.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12383539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Passive eDNA Sampling Characterizes Fish Community Assembly in the Lancang River of Yunnan, China.","authors":"Li Ding, Xinbin Duan, Mingdian Liu, Daqing Chen, Xiaofeng Huang, Dengqiang Wang, Baoshan Ma, Shijian Fu, Liqiao Zhong","doi":"10.3390/biology14081080","DOIUrl":"10.3390/biology14081080","url":null,"abstract":"<p><p>This study aimed to determine the practical efficacy of passive eDNA samplers (PEDS) for monitoring fish diversity in riverine ecosystems. It investigated the utility of environmental DNA (eDNA) in accurately depicting fish composition and diversity within the Lancang River. Environmental DNA technology, particularly PEDS, may be used as a substitute for traditional water filtration techniques. However, its effectiveness in natural water ecosystems remains to be proven. The filter materials included mixed cellulose acetate and nitrate (MCE), nylon (NL), glass fiber (GF), and polyvinyl chloride filter membrane (PVC). This study used four different types of filters, each with identical pore sizes and dimensions but constructed from various materials, to assess eDNA capture under laboratory and field conditions in the water samples. The filter materials included mixed cellulose acetate and nitrate (MCE), nylon (NL), glass fiber (GF), and polyvinyl chloride filter membrane (PVC). Environmental DNA macrobarcoding was used to analyze fish biodiversity and to understand the environmental effects on species distribution. Our study identified 50 fish species inhabiting the Lancang River, with equal representation of exotic and native species. A comparative analysis of four filter-based environmental DNA samplers and traditional environmental DNA sampling methods demonstrated comparable species richness. Redundancy analysis indicated that environmental variables, elevation, electrical conductivity, salinity, and chlorophyll-a significantly influenced the distribution patterns of both non-native and native fish species in the river. This study highlights the significance of eDNA technology in evaluating fish diversity across diverse habitats, thereby establishing a theoretical framework for the sustained monitoring and management of fish biodiversity in protected areas.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12383293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parasitic Fauna of <i>Lepus europaeus</i> and <i>Lepus timidus</i> in Kazakhstan: Parasitological Profile and Molecular Identification.","authors":"Vladimir Kiyan, Ainura Smagulova, Nurassyl Manapov, Karina Jazina, Rabiga Uakhit, Aitbay Bulashev, Lyudmila Lider, Sergey Leontyev","doi":"10.3390/biology14081083","DOIUrl":"10.3390/biology14081083","url":null,"abstract":"<p><p>Hares (<i>Lepus europaeus</i> and <i>Lepus timidus</i>) play important ecological and economic roles in Kazakhstan; however, data on their parasitic fauna are scarce. This study aimed to assess the diversity, prevalence, and genetic characteristics of endoparasites in wild hare populations from central and northern Kazakhstan. From November 2022 to February 2025, 107 hares (<i>L. europaeus</i>, n = 46; <i>L. timidus</i>, n = 61) were collected in the Akmola and Karaganda regions. Parasitological and coprological analyses were conducted. Genetic and phylogenetic analyses were performed using partial sequences of the mitochondrial <i>cox1</i> and <i>nad1</i> genes and a partial 28S rDNA region to assess the genetic diversity and evolutionary relationships of selected parasite genera. Seven parasite taxa were identified: <i>Mosgovoyia pectinata</i> (6.5% in <i>L. europaeus</i>, 11.5% in <i>L. timidus</i>), <i>Cysticercus pisiformis</i> (4.3% in <i>Le</i>, 3.3% in <i>Lt</i>), <i>Coenurus serialis</i> (3.3%, only in <i>Lt</i>), <i>Passalurus ambiguus</i> (6.5% in <i>Le</i>, 4.9% in <i>Lt</i>), <i>Nematodirus leporis</i> (36.6% in <i>Le</i>, 13.4% in <i>Lt</i>), <i>Eimeria</i> spp. (9.1% in <i>Le</i>, 3.8% in <i>Lt</i>), and <i>Trichuris leporis</i> (1.9%, only in <i>Lt</i>). Genetic methods confirmed species identity and revealed phylogenetic relationships. This is the first genetically confirmed survey of endoparasites in hares in Kazakhstan. The results contribute valuable data to regional parasitology and support the need for continued wildlife health monitoring.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12383461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distribution and Variation Characteristics of Branched Glycerol Dialkyl Glycerol Tetraethers (BrGDGTs) in Sediment Cores Along the Nearshore-to-Offshore Gradient of the East China Sea and Their Correlation with Microbial Community Diversity.","authors":"Ting Zeng, Cheng Liu, Qunhui Yang, Jingyuan Zhao, Fuwu Ji","doi":"10.3390/biology14081077","DOIUrl":"10.3390/biology14081077","url":null,"abstract":"<p><p>Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are promising molecular biomarkers widely applied in paleoenvironmental reconstructions, including temperature and pH. However, knowledge of the microorganisms responsible for brGDGT production in marine environments remains limited, which constrains the further development and application of brGDGT-based proxies for reconstructing past marine conditions. In this study, both 'living' intact polar lipid-derived brGDGTs (IPL-brGDGTs) and 'fossil' core brGDGTs (CL-brGDGTs), together with bacterial community compositions, were analysed in multiple sediment cores collected along a nearshore-to-offshore transect in the East China Sea (ECS). The potential correlations between brGDGT distributions and bacterial community compositions at varying sediment depths across an environmental gradient were also explored. Results revealed that IPL-brGDGTs were predominantly biosynthesised in situ, whereas CL-brGDGTs reflected a mixture of marine autochthonous production and terrestrial inputs. Potential brGDGT-producing bacteria in nearshore environments were primarily composed of chemolithoautotrophic taxa (e.g., Gammaproteobacteria and Dehalococcoidia) and chemoheterotrophic taxa (e.g., Alphaproteobacteria, Bacilli, and Actinobacteria). In contrast, offshore regions were dominated by chemoheterotrophic hypoxic bacteria (e.g., Anaerolineae and Phycisphaerae) and facultatively anaerobic chemolithoautotrophic bacteria (e.g., Gammaproteobacteria and Desulfobacteria). A significant difference in bacterial community composition and IPL-brGDGT distribution was observed at a depth of 17 cm, likely due to physical disturbance in near-surface sediments, such as wave action, tidal forces, and storm events. Variance partitioning analysis (VPA) revealed that the bacterial community composition alone accounted for 14.1% of the variation in IPL-brGDGTs and 6.5% in CL-brGDGTs, further suggesting that the distribution of brGDGTs is primarily influenced by the composition of the bacterial community in the nearshore-to-offshore sedimentary ecosystems of the ECS. These findings regarding the potential biosynthesis of brGDGTs in coastal habitats advance our understanding of the microbial mechanisms that regulate brGDGT distribution in marine ecosystems. Moreover, they emphasise the importance of considering physical disturbance effects when interpreting sedimentary brGDGT records for paleoenvironmental reconstructions in marginal seas, such as the ECS.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12383918/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144993986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ex Vivo Characterization of Peritoneal Macrophages from Novel ABCA1-LSL and ABCG1-LSL Mice for Macrophage-Specific ABC-Transporter Overexpression.","authors":"Jing Echesabal-Chen, Lawrence Fernando, Ally Brawner, Achala Pokhrel, Kun Huang, Rhonda Reigers Powell, Terri Bruce, Jan Guz, Fu-Lei Tang, Alexander Awgulewitsch, Alexis Stamatikos","doi":"10.3390/biology14081073","DOIUrl":"10.3390/biology14081073","url":null,"abstract":"<p><p>We aimed to characterize peritoneal macrophages from two novel mouse models that enable macrophage-specific overexpression of ABCA1 and ABCG1 via Cre recombinase. Since ABCA1/ABCG1 expression in macrophages is acknowledged to be anti-atherogenic, overexpression of these two transporters may result in a potent atheroprotective effect. However, there are no current animal models that permit overexpression of ABCA1/ABCG1 to precisely occur in macrophages. The purpose of this work was to use ex vivo strategies to characterize the peritoneal macrophages from two novel mouse models: ABCA1-LSL mice and ABCG1-LSL mice. Overexpression of ABCA1/ABCG1 in peritoneal macrophages is controlled by Cre recombinase, due to the LoxP-Stop-LoxP (LSL) system regulating ABC-transporter overexpression. In this study, we first characterized cells isolated from the peritoneal cavities of mice via immunofluorescent staining with macrophage markers CD11b and F4/80 to confirm that we were successful with peritoneal macrophage isolation. We next isolated peritoneal macrophages from ABCA1-LSL mice and ABCG1-LSL mice, and then we incubated these cells with gesicle particles containing Cre recombinase to measure ABC-transporter expression via immunoblotting and measure apoAI/HDL-mediated efflux using cholesterol efflux assays. In our experiments, we observed increases in ABCA1 protein expression and apoAI-mediated cholesterol efflux within ABCA1-LSL peritoneal macrophages, and increased ABCG1 protein expression and HDL-mediated cholesterol efflux in ABCG1-LSL peritoneal macrophages, when compared to corresponding control peritoneal macrophage groups. In conclusion, this report shows that ABCA1-LSL mice and ABCG1-LSL mice may possibly be utilized to cross with macrophage-specific Cre mice to study ABC-transporter overexpression precisely in macrophages, thereby providing valuable tools to dissect the impact of macrophage-specific ABC-transporter overexpression on atherogenesis.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12383658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144993459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Paternal Cocaine Exposure and Its Testicular Legacy: Epigenetic, Physiological, and Intergenerational Consequences.","authors":"Candela R González, Betina González","doi":"10.3390/biology14081072","DOIUrl":"10.3390/biology14081072","url":null,"abstract":"<p><p>Cocaine use remains a major public health concern, with rising global prevalence and a well-established profile of neurotoxicity and addictive potential. While the central nervous system has been the primary focus of cocaine research, emerging evidence indicates that cocaine also disrupts male reproductive physiology. In the testis, cocaine alters the endocrine microenvironment, induces cell-specific damage, and disrupts spermatogenesis. Cocaine also interferes with epigenetic programming in germ cells and mature sperm, potentially leading to heritable epimutations. Epidemiology data reveal that approximately two-thirds of regular cocaine users are males of reproductive age, and preclinical models have documented numerous behavioral and molecular alterations in their offspring, often linked to paternal cocaine exposure-such as increased drug resistance or vulnerability, altered anxiety-like behavior, impaired learning/memory, disrupted social behaviors, and shifts in neural circuitry and gene expression in reward-related brain regions. This review aims to integrate findings from studies that have independently examined testicular dysfunction, germline epigenetic reprogramming, and offspring outcomes, offering a unified perspective on their potential interconnections and highlighting future directions for research in the field of epigenetic inheritance.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12383874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nucleotide Metabolism and Immune Genes Can Predict the Prognostic Risk of Hepatocellular Carcinoma and the Immune Microenvironment.","authors":"Xiaofang Wang, Qinghua Cui, Yuan Zhou","doi":"10.3390/biology14081079","DOIUrl":"10.3390/biology14081079","url":null,"abstract":"<p><p>The overall survival of hepatocellular carcinoma (HCC) remains poor, highlighting the need for better prognostic tools. Nucleotide metabolism fuels tumor progression, while the immune microenvironment dictates therapy response, but integrated models combining both features are lacking. Using TCGA-LIHC transcriptomic/clinical data, we identified nucleotide metabolism and immune-related differentially expressed genes (NMIRGs), which stratified HCC patients into two subtypes via non-negative matrix factorization. A nine-gene prognostic risk signature was constructed through LASSO/Cox regression and validated using independent GEO datasets, and the NMIRG signature was further validated experimentally via RT-qPCR in HCC cell lines and independently using the HPA database for protein-level evidence. As evaluated by our risk signature, high-risk patients exhibited altered immune profiles (T cells increasing, neutrophils decreasing), elevated tumor mutation burden and microsatellite instability, and worse predicted immunotherapy response. Gene set enrichment analysis linked high-risk genes to immune pathways and low-risk genes to metabolic processes. Our risk signature predicted HCC prognosis independent of demographic features and outperformed existing signatures with superior C-index accuracy, effectively predicting immune microenvironment status and therapy benefits. Together, this integrated NMIRG signature offers enhanced prognostication and identifies promising biomarkers for personalized HCC management.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12383802/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}