Functional & Integrative Genomics最新文献

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Analyzing the potential targets and mechanism of per- and polyfluoroalkyl substances (PFAS) on breast cancer by integrating network toxicology, single-cell sequencing, spatial transcriptomics, and molecular simulation. 结合网络毒理学、单细胞测序、空间转录组学和分子模拟等方法,分析全氟烷基和多氟烷基物质(PFAS)对乳腺癌的潜在靶点和作用机制。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2025-06-04 DOI: 10.1007/s10142-025-01616-y
Jiajun Li, Deqi Wang, Sihan Song, Yi Wang, Xinlei Wu, Zhuoyi Du, Yanggang Hong
{"title":"Analyzing the potential targets and mechanism of per- and polyfluoroalkyl substances (PFAS) on breast cancer by integrating network toxicology, single-cell sequencing, spatial transcriptomics, and molecular simulation.","authors":"Jiajun Li, Deqi Wang, Sihan Song, Yi Wang, Xinlei Wu, Zhuoyi Du, Yanggang Hong","doi":"10.1007/s10142-025-01616-y","DOIUrl":"https://doi.org/10.1007/s10142-025-01616-y","url":null,"abstract":"<p><p>Per- and polyfluoroalkyl substances (PFAS), particularly perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS), are persistent environmental contaminants linked to adverse health effects, including an increased risk of breast cancer. However, the molecular mechanisms through which PFAS contribute to breast cancer development remain poorly understood. In this study, we employed an integrated approach combining network toxicology, single-cell sequencing, spatial transcriptomics, and molecular simulation to investigate the effects of PFAS on breast cancer. By constructing a protein-protein interaction (PPI) network, we identified six core genes (PPARG, CD36, FABP4, PPARGC1A, LPL, and PCK1) that play a significant role in the development of breast cancer. These genes are involved in key cellular processes such as lipid metabolism, oxidative phosphorylation, and immune regulation, all of which are disrupted by PFAS exposure. Single-cell and spatial transcriptomic analyses revealed that these genes are predominantly expressed in endothelial, myeloid, and cancer-associated fibroblasts within the tumor microenvironment. Molecular simulation further confirmed strong binding energies between PFAS and these target proteins, suggesting direct interactions. Our findings provide novel insights into how PFAS may promote breast cancer progression at the molecular level and highlight the need for further research on environmental pollutants in cancer risk assessment and public health initiatives.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"119"},"PeriodicalIF":3.9,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Selenium deficiency is functionally linked with the molecular etiopathogenesis of necrotizing enterocolitis (NEC). 硒缺乏在功能上与坏死性小肠结肠炎(NEC)的分子发病机制有关。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2025-06-03 DOI: 10.1007/s10142-025-01628-8
Kubilay Gürünlüoğlu, Muhammed Dündar, Turgay Ünver, Hatice Turgut, Semra Gürünlüoğlu, Necmettin Akpınar, Hasan Ateş, Ramazan Özdemir, Turan Yıldız, Mehmet Demircan, Mehmet Aslan, Ahmet Koç
{"title":"Selenium deficiency is functionally linked with the molecular etiopathogenesis of necrotizing enterocolitis (NEC).","authors":"Kubilay Gürünlüoğlu, Muhammed Dündar, Turgay Ünver, Hatice Turgut, Semra Gürünlüoğlu, Necmettin Akpınar, Hasan Ateş, Ramazan Özdemir, Turan Yıldız, Mehmet Demircan, Mehmet Aslan, Ahmet Koç","doi":"10.1007/s10142-025-01628-8","DOIUrl":"10.1007/s10142-025-01628-8","url":null,"abstract":"<p><p>Necrotizing enterocolitis (NEC) is a severe and often catastrophic gastrointestinal emergency that predominantly affects neonates, especially those born prematurely, and is associated with high rates of morbidity and mortality. Despite its significant clinical impact, the precise etiology and molecular pathogenesis of NEC remain incompletely understood. In this study, we conducted global transcriptomic profiling using high-throughput RNA sequencing in 11 premature neonates diagnosed with NEC, following rigorous inclusion and exclusion criteria. Compared to healthy controls, we identified 1,204 differentially expressed genes (DEGs), including 636 upregulated and 568 downregulated transcripts. Notably, genes involved in hypoxia-induced apoptosis (e.g., HIF1 AAS3, HIF1 AAS1), the caspase cascade (BCL2, BCL6, CASP5, CASP7), and inflammation (IL1RAP, IL6ST, TNFAIP3, TNFRSF10 A, TLR6, TLR10) were significantly upregulated. In contrast, IL18, a key modulator of inflammatory responses, was downregulated. Interestingly, several genes encoding selenoproteins (GPX1, GPX4, SELENON, SELENOM, SELENOF, SELENOW, SELENOT) were also downregulated, suggesting molecular evidence of selenium deficiency. Gene ontology and pathway enrichment analyses revealed widespread dysregulation in pathways related to hypoxia response, systemic inflammation, coagulation, antimicrobial defense, mitochondrial function, autophagy, selenium metabolism, and apoptosis. Collectively, our findings provide novel insights into the molecular underpinnings of NEC in premature infants and suggest that systemic hypoxia, oxidative stress, selenium deficiency, and programmed cell death contribute significantly to its pathogenesis.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"118"},"PeriodicalIF":3.9,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12134042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A novel oncogene, leucine-rich repeat protein 1, mediates hypoxia-induced hepatocellular carcinoma progression. 一种新的致癌基因,富含亮氨酸的重复蛋白1,介导缺氧诱导的肝细胞癌进展。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2025-06-03 DOI: 10.1007/s10142-025-01626-w
Li Tao, Yixian Guo, Runkun Liu, Meng Lv, Yufeng Wang
{"title":"A novel oncogene, leucine-rich repeat protein 1, mediates hypoxia-induced hepatocellular carcinoma progression.","authors":"Li Tao, Yixian Guo, Runkun Liu, Meng Lv, Yufeng Wang","doi":"10.1007/s10142-025-01626-w","DOIUrl":"https://doi.org/10.1007/s10142-025-01626-w","url":null,"abstract":"<p><p>The involvement of leucine rich repeats protein 1 (LRR1) in various biological processes has been established, but its specific role and potential mechanisms in hepatocellular carcinoma (HCC) remain unclear. The aim of this study was to explore the potential expression, function, and mechanisms of LRR1 in HCC. Data acquired from TCGA, GEO and other online databases was used to investigate the expression and roles of LRR1 in HCC through various approaches, including expression profiling, clinical significance analysis, methylation status examination, immune infiltration assessment, genomic mutation analysis, and pathway network exploration. With findings in bioinformatic analysis, we further validated the involvement of LRR1 in HCC progression by cellular experiments. The expression of LRR1 is significantly upregulated in HCC compared to normal liver tissues and cell line. Additionally, the involvement of LRR1 was implicated in various modifications across diverse aspects associated with HCC. Enrichment analysis indicated that LRR1 was induced by hypoxia in HIF-1-dependent manner. The cell experiments convincingly demonstrated the pivotal role of LRR1 in tumor cell proliferation, migration, invasion and angiogenesis under the regulation of HIF-1. Our findings demonstrate a novel oncogene LRR1 in HCC, which is also a HIF-1 target gene and functions as a promising biomarker and contributes to the hypoxia-induced progression of HCC through a HIF-1/LRR1 manner.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"117"},"PeriodicalIF":3.9,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An efficient hairy root system for validation of CRISPR/Cas system activities in cotton. 棉花毛状根系中CRISPR/Cas系统活性验证
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2025-06-02 DOI: 10.1007/s10142-025-01627-9
Manyu Zhang, Lili Zhou, Mahideen Afridi, Huiming Guo, Hongmei Cheng
{"title":"An efficient hairy root system for validation of CRISPR/Cas system activities in cotton.","authors":"Manyu Zhang, Lili Zhou, Mahideen Afridi, Huiming Guo, Hongmei Cheng","doi":"10.1007/s10142-025-01627-9","DOIUrl":"https://doi.org/10.1007/s10142-025-01627-9","url":null,"abstract":"<p><p>The hairy root induction system has been widely applied in studying gene expression and function in plant species due to its rapidity and efficiency. The hairy root system is an efficient tool for evaluating the activities of CRISPR/Cas systems. Cotton hairy roots were primarily induced through cotton tissue culture under aseptic conditions and by injecting cotton stem tips under non-aseptic conditions. However, both methods are lab-intensive and time-consuming. In this study, an efficient cotton hairy root induction procedure was established via infecting cotton hypocotyls with Agrobacterium rhizogenes under non-sterile conditions. Cotton seedlings with expanded cotyledons were decapitated with a slanted cut, and the residual hypocotyl (maintained 1 cm apical portion) was inoculated with A. rhizogenes. Over 90% of the infected explants from all three tested varieties could produce hairy roots after 8 days of inoculation. The effictiveness of the method was tested by overexpressing two reporter genes (eGFP and GUS). The transformation efficiency of the GUS and eGFP were ranged from50-68.18% and 40.9-68.18%. In addition, the editing efficiency of target sites in different CRISPR/Cas systems were also tested in hairy root. This method provided technical support for screening suitable target sites for cotton gene editing.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"116"},"PeriodicalIF":3.9,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144197975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Functional genomics reveals adipose-kidney crosstalk as a contributor to kidney fibrosis via the OSM-OSMR pathway. 功能基因组学揭示,脂肪-肾脏串扰通过osmm - osmr途径促进肾脏纤维化。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2025-06-02 DOI: 10.1007/s10142-025-01624-y
Jing Zhang, Zhaojun Liu, Shihui Dong, Kun Xu, Kangchun Wang, Luyu Gong, Qiaoqiao Liu, Yue Guo, Yeping Zhu, Jingrong She, Song Jiang, Shaolin Shi, Zhihong Liu, Jingping Yang
{"title":"Functional genomics reveals adipose-kidney crosstalk as a contributor to kidney fibrosis via the OSM-OSMR pathway.","authors":"Jing Zhang, Zhaojun Liu, Shihui Dong, Kun Xu, Kangchun Wang, Luyu Gong, Qiaoqiao Liu, Yue Guo, Yeping Zhu, Jingrong She, Song Jiang, Shaolin Shi, Zhihong Liu, Jingping Yang","doi":"10.1007/s10142-025-01624-y","DOIUrl":"https://doi.org/10.1007/s10142-025-01624-y","url":null,"abstract":"<p><p>Kidney injury is a severe complication of type 2 diabetes, yet its pathophysiology varies among patients. Although abnormal adipose has been identified as an indicator for the risk of kidney injury in type 2 diabetes, the underlying mechanisms remain unclear. Here, we integrated adipose functional genomics and genome-wide association studies of diabetic nephropathy (DN) to investigate the relationship between adipose and kidney injury. By generating the epigenome, transcriptome and regulatome, we constructed functional genomics map of adipose, revealing the regulatory role of perirenal adipose tissue in kidney disease. Integration of the functional genomics with genetic risk demonstrated that the genetic risk of DN is mediated not only through the kidney itself but also via adipose-kidney crosstalk. Our results revealed that risk variant rs2412980 functions through an adipose-specific regulatory element to control the expression of OSM, encoding the cytokine oncostatin-M. Adipose-derived OSM can reprogram OSMR-expressing renal fibroblasts, and subsequent activation of OSM-OSMR pathway is associated with advanced kidney injury, including reduced eGFR, elevated proteinuria and creatinine levels. Our work confirmed the linkage between adipose and kidney diseases with the genetic evidence, and revealed that the adipo-renal axis promotes the fibrosis of kidney under diabetes through the OSM-OSMR pathway.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"114"},"PeriodicalIF":3.9,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144197976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
LSINCT5: a pivotal oncogenic long non-coding RNA in cancers. LSINCT5:癌症中关键的致癌长链非编码RNA。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2025-06-02 DOI: 10.1007/s10142-025-01610-4
Sharanya K Sritharan, Amar Harris Arifin, Shamala Salvamani, Rhun Yian Koh, Baskaran Gunasekaran
{"title":"LSINCT5: a pivotal oncogenic long non-coding RNA in cancers.","authors":"Sharanya K Sritharan, Amar Harris Arifin, Shamala Salvamani, Rhun Yian Koh, Baskaran Gunasekaran","doi":"10.1007/s10142-025-01610-4","DOIUrl":"https://doi.org/10.1007/s10142-025-01610-4","url":null,"abstract":"<p><p>Long stress-induced non-coding transcript 5 (LSINCT5) is a long non-coding RNA (lncRNA) that has been demonstrated to exhibit oncogenic properties as its upregulation was found to be commonly associated with malignant clinicopathological features in various cancers. Numerous studies have reported that LSINCT5 overexpression may promote cancer progression by regulating the expression of genes that modulate important aspects of cell activity and by interfering with signalling pathways via precise mechanisms such as microRNA (miRNA) sponging, protein interactions, as well as acting as a downstream target of transcription factors. Eventually, these processes stimulate malignant behaviour such as proliferation, invasion, migration, and epithelial-mesenchymal transition (EMT). Research suggests LSINCT5 could be a useful biomarker and therapeutic target. However, understanding their complex nature and impact on physiological processes is crucial for determining their oncogenic properties and potential use in therapy. This review focuses on LSINCT5's biological functions, expression patterns, oncogenic roles, and molecular mechanisms in cancers. We further highlight the potential of LSINCT5 as a biomarker for early diagnosis and prognosis, as well as a therapeutic target in cancer therapy.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"115"},"PeriodicalIF":3.9,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144197977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genome-wide characterization of GRF-GIF transcriptional modules in kenaf (Hibiscus cannabinus L.) reveals their roles in plant development and multi-stress adaptation. 红麻(Hibiscus cannabinus L.) GRF-GIF转录模块的全基因组特征揭示了其在植物发育和多逆境适应中的作用。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2025-05-30 DOI: 10.1007/s10142-025-01622-0
Jiao Yue, Qijing Wu, Yuqi Tan, Qiuping Wang, Rujian Wei, Xu Wang, Tao Chen, Dengjie Luo, Peng Chen
{"title":"Genome-wide characterization of GRF-GIF transcriptional modules in kenaf (Hibiscus cannabinus L.) reveals their roles in plant development and multi-stress adaptation.","authors":"Jiao Yue, Qijing Wu, Yuqi Tan, Qiuping Wang, Rujian Wei, Xu Wang, Tao Chen, Dengjie Luo, Peng Chen","doi":"10.1007/s10142-025-01622-0","DOIUrl":"https://doi.org/10.1007/s10142-025-01622-0","url":null,"abstract":"<p><p>Growth regulatory factors (GRFs) are pivotal regulators of plant growth, development, and stress responses, functioning synergistically with GRF-interacting factors (GIFs) as transcriptional co-activators. Despite their characterization in diverse plants, GRF and GIF families remain unstudied in kenaf (Hibiscus cannabinus). Here, 33 HcGRF and 7 HcGIF genes were systematically identified from the kenaf genome. Phylogenetic analysis classified HcGRF into 10 subgroups (11 in clade F) and HcGIF into 3 subgroups. Promoter cis-element analysis revealed enrichment in abiotic stress response elements, light-response elements, and hormone response elements in the GRF and GIF promoter region. Based on RNA-Seq data, tissue-specific expression profiling demonstrated predominant accumulation of most HcGRFs (notably HcGRF3 and HcGRF21) and HcGIF1 in leaves and buds, and that the expression of HcGRF3, HcGFR21, and HcGIF1 was 5-fold, 14.7-fold, and 11.3-fold higher than that of leaves, respectively, suggesting that they play a central role in the regulation of growth regulation. Transcriptome-wide interrogation under chromium, salinity, cadmium, and drought stresses revealed spatiotemporal expression divergence. qRT-PCR confirmed that HcGRF3 expression increased gradually under salt/drought stress, while HcGRF21 and HcGIF1 peaked at 12 h. Subcellular localization confirmed nuclear targeting of these genes. In addition, physiological and biochemical analyses through functional validation by VIGS and transgenic Arabidopsis thaliana showed that salt and drought tolerance of kenaf was reduced by gene silencing, whereas overexpression plants showed stronger tolerance. The novelty and significance of these findings for kenaf on the roles of HcGRFs and HcGIFs genes in the growth, development, and abiotic stresses.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"112"},"PeriodicalIF":3.9,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The CRISPR-Cas revolution in head and neck cancer: a new era of targeted therapy. 头颈癌的CRISPR-Cas革命:靶向治疗的新时代。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2025-05-30 DOI: 10.1007/s10142-025-01612-2
Mohsen Hashemi, Xaniar Mohmmadi Khanaghah, Javid Sadri Nahand
{"title":"The CRISPR-Cas revolution in head and neck cancer: a new era of targeted therapy.","authors":"Mohsen Hashemi, Xaniar Mohmmadi Khanaghah, Javid Sadri Nahand","doi":"10.1007/s10142-025-01612-2","DOIUrl":"https://doi.org/10.1007/s10142-025-01612-2","url":null,"abstract":"<p><p>Head and neck cancer (HNC) encompasses a diverse array of malignancies impacting the anatomical structures of the head and neck region, ranking as the seventh most prevalent cancer type globally. The occurrence and advancement of HNC are intricately linked to mutations and disruptions within critical signaling pathways, accentuating the imperative for targeted therapeutic interventions to rectify these genetic aberrations. Traditional treatment modalities, including surgical intervention and adjuvant chemotherapy or radiotherapy, frequently culminate in considerable morbidity and suboptimal prognoses. Recently, the CRISPR-Cas system has emerged as a revolutionary gene-editing platform, poised to redefine therapeutic approaches in gene therapy and oncological research. Despite its potential, CRISPR-Cas faces challenges such as off-target effects, delivery inefficiencies, and immunogenicity, which must be addressed for clinical success. This review meticulously evaluates the progress in CRISPR-Cas technologies aimed at targeting essential signaling pathways implicated in HNC, addressing current challenges while highlighting optimal targets, Cas nucleases, and innovative delivery mechanisms, thereby elucidating the therapeutic potential and clinical applicability of the CRISPR-Cas paradigm in the management of HNC.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"113"},"PeriodicalIF":3.9,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Decoding fungal communication networks: molecular signaling, genetic regulation, and ecological implications. 解码真菌通讯网络:分子信号,遗传调控和生态影响。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2025-05-29 DOI: 10.1007/s10142-025-01620-2
Shumila Ishfaq, Hadiqa Anum, Tayyaba Shaheen, Sana Zulfiqar, Anila Ishfaq, Arslan Anjum, Umera Ramzan, Amna Rafiq, Mehboob-Ur-Rahman, Wei Guo
{"title":"Decoding fungal communication networks: molecular signaling, genetic regulation, and ecological implications.","authors":"Shumila Ishfaq, Hadiqa Anum, Tayyaba Shaheen, Sana Zulfiqar, Anila Ishfaq, Arslan Anjum, Umera Ramzan, Amna Rafiq, Mehboob-Ur-Rahman, Wei Guo","doi":"10.1007/s10142-025-01620-2","DOIUrl":"https://doi.org/10.1007/s10142-025-01620-2","url":null,"abstract":"<p><p>Fungal communication networks regulate essential biological processes, enabling fungi to adapt to environmental changes, coordinate development, and establish interactions within microbial communities. These networks are mediated by diverse signaling molecules, including volatile organic compounds (VOCs), peptide signaling molecules, and quorum-sensing molecules, which facilitate intra- and interspecies communication. The intricate regulation of these signals occurs through specialized signal transduction pathways such as G-protein-coupled receptors (GPCRs) and two-component regulatory systems, allowing fungi to sense external cues and modulate their physiological responses. Genetic mechanisms also play a critical role in fungal communication, influencing community dynamics through regulatory genes governing hyphal fusion, pheromone signaling, and secondary metabolite biosynthesis. Crosstalk between these signaling pathways is further modulated by epigenetic modifications, which fine-tune gene expression in response to environmental conditions. The integration of these molecular networks shapes fungal interactions, impacting resource acquisition, symbiosis, and pathogenicity. Additionally, fungal communication has significant ecological and evolutionary implications, contributing to niche establishment, microbial competition, and host-pathogen interactions. Despite significant progress in understanding fungal communication, key knowledge gaps remain regarding the interplay between signaling molecules, genetic regulation, and environmental adaptation. Future research should focus on unraveling the molecular mechanisms underlying fungal signaling networks and their potential applications in biotechnology, agriculture, and medicine. Harnessing fungal communication could lead to novel strategies for improving crop protection, developing antifungal therapies, and optimizing industrial fermentation processes. This review synthesizes recent advancements in fungal signaling research, providing a comprehensive perspective on its complexity and evolutionary significance.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"111"},"PeriodicalIF":3.9,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Zebrafish metabolomics: a comprehensive approach to understanding health and disease. 斑马鱼代谢组学:了解健康和疾病的综合方法。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2025-05-28 DOI: 10.1007/s10142-025-01621-1
A Vivekaa, Jayshree Nellore, Swetha Sunkar
{"title":"Zebrafish metabolomics: a comprehensive approach to understanding health and disease.","authors":"A Vivekaa, Jayshree Nellore, Swetha Sunkar","doi":"10.1007/s10142-025-01621-1","DOIUrl":"https://doi.org/10.1007/s10142-025-01621-1","url":null,"abstract":"<p><p>Zebrafish (Danio rerio) have become a valuable model in biomedical research due to their genetic similarity to humans, rapid development, and suitability for high-throughput studies. Metabolomic analyses in zebrafish provide critical insights into the biochemical pathways underlying health and disease. This review explores the applications of metabolomics in zebrafish research, highlighting its contributions to understanding embryonic development, tuberculosis, neurodegenerative disorders such as Alzheimer's disease, obesity-related metabolic dysfunction, and drug-induced toxicity through a thorough literature review. Zebrafish metabolomics reveals dynamic metabolite shifts during vertebrate development. In tuberculosis research, zebrafish models have helped identify metabolic biomarkers with potential translational relevance. Studies on Alzheimer's disease suggest that metabolomics can elucidate neuroprotective mechanisms, while investigations into obesity have provided insights into metabolic imbalances associated with kidney dysfunction. Furthermore, toxicometabolomic studies have demonstrated the utility of zebrafish in assessing drug-induced renal injury. Despite their advantages, zebrafish metabolomics faces challenges, including differences in metabolic rates compared to mammals, the need for standardized protocols, and limitations in metabolite database annotations. Nonetheless, integrating metabolomics with other omics approaches holds great promise for advancing disease research and paving the way for personalized medicine.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"110"},"PeriodicalIF":3.9,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144155454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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