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Identification of ascorbate peroxidase family genes reveals expression of TkAPX250a confers heat stress tolerance in Taraxacum kok-saghyz 抗坏血酸过氧化物酶家族基因的鉴定表明,TkAPX250a基因的表达使紫杉树具有耐热性。
IF 2.4 3区 生物学
Gene Pub Date : 2026-02-20 Epub Date: 2025-11-25 DOI: 10.1016/j.gene.2025.149918
Shiqi Long, Boxuan Yuan, Minmin He, Guoen Ao, Baoqiang Wang, Xuchu Wang
{"title":"Identification of ascorbate peroxidase family genes reveals expression of TkAPX250a confers heat stress tolerance in Taraxacum kok-saghyz","authors":"Shiqi Long,&nbsp;Boxuan Yuan,&nbsp;Minmin He,&nbsp;Guoen Ao,&nbsp;Baoqiang Wang,&nbsp;Xuchu Wang","doi":"10.1016/j.gene.2025.149918","DOIUrl":"10.1016/j.gene.2025.149918","url":null,"abstract":"<div><div>Ascorbate peroxidase (APX) enzymes are pivotal in scavenging reactive oxygen species (ROS) and maintaining redox homeostasis in plants, a function critical for survival under abiotic stress conditions. To investigate this key enzyme system in the rubber-producing dandelion <em>Taraxacum kok-saghyz</em> (Tk)—an emerging model for sustainable rubber production—we conducted a genome-wide analysis of its APX genes. We identified seven TkAPX genes, whose predicted subcellular localizations include the cytoplasm, plasma membrane, and chloroplasts. Promoter analysis revealed an abundance of stress-responsive motifs, supporting their potential role in stress adaptation. By integrating time-course qPCR of the TkAPX family under heat stress with transcriptome-wide expression profiling across tissues, we identified <em>TkAPX250a</em> as a pivotal candidate. This gene showed a remarkable ∼ 20-fold increase in transcript levels in subsequent transgenic lines compared to wild-type controls, confirming highly efficient transgene expression without silencing. Under thermal stress, these transgenic lines exhibited reduced ROS accumulation and membrane lipid peroxidation while maintaining higher chlorophyll content and biomass, demonstrating that TkAPX250a coordinately enhances thermotolerance and photosynthetic stability. Mechanistically, <em>TkAPX250a</em> overexpression not only enhanced APX activity and lowered H<sub>2</sub>O<sub>2</sub> accumulation but also synergistically upregulated the activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD). Time-resolved assays under heat stress further delineated a stratified antioxidant hierarchy within this coordinated response, with SOD and CAT acting as core responders. These findings establish TkAPX250a as a central genetic regulator in abiotic stress adaptation and provide a molecular basis for breeding stressresilient rubber crops, addressing a critical need in agriculture under changing climate conditions.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"980 ","pages":"Article 149918"},"PeriodicalIF":2.4,"publicationDate":"2026-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145632207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Two transcription factors and one antisense RNA underlie the thermoregulated insect pathogenicity of Yersinia entomophaga MH96 两个转录因子和一个反义RNA是虫食耶尔森菌MH96热调控昆虫致病性的基础。
IF 2.4 3区 生物学
Gene Pub Date : 2026-02-20 Epub Date: 2025-12-11 DOI: 10.1016/j.gene.2025.149955
Amber R. Paulson , Maureen O’Callaghan , Xue-Xian Zhang , Naran Naren , Marion Schoof , Mark R.H. Hurst
{"title":"Two transcription factors and one antisense RNA underlie the thermoregulated insect pathogenicity of Yersinia entomophaga MH96","authors":"Amber R. Paulson ,&nbsp;Maureen O’Callaghan ,&nbsp;Xue-Xian Zhang ,&nbsp;Naran Naren ,&nbsp;Marion Schoof ,&nbsp;Mark R.H. Hurst","doi":"10.1016/j.gene.2025.149955","DOIUrl":"10.1016/j.gene.2025.149955","url":null,"abstract":"<div><div>Entomopathogenic bacteria express virulence genes in a temperature-dependent manner, but the underlying molecular mechanisms remain poorly understood. Here, we describe the roles of an unusual LytTR-containing transcription factor Yen6 in determining the virulence of <em>Yersinia entomophaga</em> (MH96). An initial transcriptome analysis <em>in vivo</em> revealed that <em>yen6</em>, located 1,372 bp upstream from genes encoding the Yen Toxin complex (Yen-Tc), exhibited significantly higher transcriptional activity at 37 °C compared to 25 °C (adjusted <em>p</em>-value &lt; 0.001) during intrahemocoelic infection in the insect model <em>Galleria‍ mellonella</em>. Deletion of <em>yen6</em> also significantly reduced MH96′s virulence in <em>G.‍‍ mellonella</em> by up to three-fold. Next, comparing the transcriptome of wild-type MH96 and its derived Δ<em>yen6</em> mutant revealed genes for ribose utilization were downregulated whereas genes for fructose utilization and the RNA-binding protein YhbY were upregulated in the <em>yen6-</em>deficient mutant. Subsequent electromobility shift assays showed that purified Yen6<sub>His6</sub> protein was capable of specifically binding to the promoter regions of the ribose and fructose utilization-related gene clusters, as well as <em>yhbY</em>. A 645-nucleotide-long 3′ untranslated region, designated <em>yen7_AS</em>, was identified extending from the <em>yen6</em> coding region. Notably, <em>yen7_AS</em> completely overlaps the <em>yen7</em> gene on the opposing strand and may therefore act as a <em>cis</em> anti-sense RNA regulating <em>yen7</em> expression, which encodes a putative transcriptional regulator of the Yen-Tc. This study highlights the critical role of the <em>yen6–yen7</em> locus in MH96 virulence during <em>G.‍ mellonella</em> infection<em>,</em> including the complex mechanisms controlling insecticidal exoprotein production.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"980 ","pages":"Article 149955"},"PeriodicalIF":2.4,"publicationDate":"2026-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145752086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Age-induced gene expression in Thoroughbred horse skeletal muscle highlights genes that enhance muscle architecture and function 纯种马骨骼肌中年龄诱导的基因表达突出了增强肌肉结构和功能的基因。
IF 2.4 3区 生物学
Gene Pub Date : 2026-02-20 Epub Date: 2025-12-15 DOI: 10.1016/j.gene.2025.149951
Mian Feng , Thomas J. Hall , David E. MacHugh , Lisa M. Katz , Emmeline W. Hill
{"title":"Age-induced gene expression in Thoroughbred horse skeletal muscle highlights genes that enhance muscle architecture and function","authors":"Mian Feng ,&nbsp;Thomas J. Hall ,&nbsp;David E. MacHugh ,&nbsp;Lisa M. Katz ,&nbsp;Emmeline W. Hill","doi":"10.1016/j.gene.2025.149951","DOIUrl":"10.1016/j.gene.2025.149951","url":null,"abstract":"<div><div>Early skeletal muscle development is critical for young racehorses, yet research on the transcriptional changes during this period is limited. Additionally, the impact of age on the transcriptional response to exercise training in equine athletes is not well understood. A transcriptome-wide analysis of differential gene expression in skeletal muscle was performed for five untrained Thoroughbred horses sampled at rest at two years old (UR2) and three years old (UR3). A total of 136 differentially expressed genes (DEGs) were identified, with 95 increased and 41 decreased in expression. GO enrichment analysis revealed that the DEGs were primarily associated with terms related to muscle assembly and system development, including <em>Developmental process (GO:0032502</em>)<em>, Anatomical structure development (GO:0048856</em>)<em>, Actin cytoskeleton (GO:0015629</em>)<em>, and Growth factor binding (GO:0019838</em>)<em>.</em> KEGG pathway analysis indicated that <em>ECM-receptor interaction</em>, <em>Protein digestion and absorption</em>, <em>Focal adhesion</em>, and <em>PI3K-Akt signalling pathway</em> were the significant functional pathways. Protein-protein interaction network and hub gene analyses identified seven key regulatory genes: <em>COL1A1, COL1A2, COL3A1, S100A4, NOTCH1, THY1</em> and <em>MT-ND2.</em> In addition, the <em>MSTN, COL4A1, COL4A2, SPEN, S100A4, NOTCH1, NOTCH3, and THY1</em> genes were found to play key roles in the functional development of skeletal muscle. This study provides insight into the transcriptional landscape of skeletal muscle development in young Thoroughbred horses. The period between two and three years of age represents a crucial stage in skeletal muscle adaptation in the juvenile horse, with a particular emphasis on muscle structural and functional integrity.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"980 ","pages":"Article 149951"},"PeriodicalIF":2.4,"publicationDate":"2026-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145774290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 association study of tolerance to acute hypoxia in the olive flounder (Paralichthys olivaceus) using individual blood cortisol levels as a physiological phenotype 橄榄比目鱼对急性缺氧耐受性的全基因组关联研究,使用个体血液皮质醇水平作为生理表型
IF 2.4 3区 生物学
Gene Pub Date : 2026-02-20 Epub Date: 2025-12-11 DOI: 10.1016/j.gene.2025.149952
M.A.H. Dilshan , Gaeun Kim , W.K.M. Omeka , D.S. Liyanage , H.M.V. Udayantha , D.C.G. Rodrigo , G.A.N.P. Ganepola , H.A.C.R. Hanchapola , Y.K. Kodagoda , Po Gong , Jihun Lee , Sukkyoung Lee , Jeongeun Kim , Jehee Lee
{"title":"Genome-wide association study of tolerance to acute hypoxia in the olive flounder (Paralichthys olivaceus) using individual blood cortisol levels as a physiological phenotype","authors":"M.A.H. Dilshan ,&nbsp;Gaeun Kim ,&nbsp;W.K.M. Omeka ,&nbsp;D.S. Liyanage ,&nbsp;H.M.V. Udayantha ,&nbsp;D.C.G. Rodrigo ,&nbsp;G.A.N.P. Ganepola ,&nbsp;H.A.C.R. Hanchapola ,&nbsp;Y.K. Kodagoda ,&nbsp;Po Gong ,&nbsp;Jihun Lee ,&nbsp;Sukkyoung Lee ,&nbsp;Jeongeun Kim ,&nbsp;Jehee Lee","doi":"10.1016/j.gene.2025.149952","DOIUrl":"10.1016/j.gene.2025.149952","url":null,"abstract":"<div><div>Hypoxia, caused by reduced dissolved oxygen (DO) levels in water, is a critical challenge in aquaculture and often results in stress, anorexia, and mass mortality in fish. The olive flounder (<em>Paralichthys olivaceus</em>) is a key species in South Korea’s global aquaculture exports. However, aquaculture production of <em>P. olivaceus</em> experiences significant economic losses caused by hypoxia-induced fish mortality, highlighting the critical need for developing genetically improved hypoxia-tolerant strains. In this study, a genome-wide association study (GWAS) was performed to unveil single-nucleotide polymorphisms (SNPs) associated with acute hypoxia tolerance and elucidate underlying regulatory mechanisms. A total of 382 <em>P. olivaceus</em> fish were measured for blood serum cortisol level using enzyme-linked immunosorbent assay (ELISA) upon acute hypoxia stress. Blood plasma cortisol levels were used as a proxy phenotype of hypoxia tolerance, with the hypothesis that elevated concentrations indicate low tolerance, and minimized concentrations indicate high tolerance to acute hypoxia stress. Then, fish were genotyped using the Affymetrix® Axiom® myDesign™ genotype array, and 57,651 SNPs were retained after quality control filtering. A significant SNP was identified on chromosome 15 of the <em>P. olivaceus</em> genome, above the suggestive threshold (<em>p</em> &lt; 1 × 10<sup>−4</sup>) for the stress cortisol level trait. A strongly associated SNP with accession number AX-419149718 was located in the zona pellucida-like domain-containing protein 1 (<em>Zpld1</em>) gene. Gene ontology (GO) analysis suggests that <em>Zpld1</em> is involved in signaling pathways, including the integrin-mediated signaling pathway, thereby contributing to the mitigation of hypoxia stress effects. Collectively, this study provides insights into the genetic basis of acute hypoxia tolerance in <em>P. olivaceus</em> and may serve as a foundation for establishing genomic selection of olive flounders with acute hypoxia stress tolerance in aquaculture breeding programs.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"980 ","pages":"Article 149952"},"PeriodicalIF":2.4,"publicationDate":"2026-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145735922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Differential genomic signatures of homozygosity and a haplotype sharing Extents across breeds associated with body size variation in Korean indigenous goats 韩国本土山羊体型变异与品种间纯合子性和单倍型共享程度的差异基因组特征。
IF 2.4 3区 生物学
Gene Pub Date : 2026-02-20 Epub Date: 2025-12-11 DOI: 10.1016/j.gene.2025.149956
Seongmin Kim , Hankyeol Jeong , Ga-Eun Kim , Kwan-Woo Kim , Woncheoul Park , Jaemin Kim , Bong-Hwan Choi
{"title":"Differential genomic signatures of homozygosity and a haplotype sharing Extents across breeds associated with body size variation in Korean indigenous goats","authors":"Seongmin Kim ,&nbsp;Hankyeol Jeong ,&nbsp;Ga-Eun Kim ,&nbsp;Kwan-Woo Kim ,&nbsp;Woncheoul Park ,&nbsp;Jaemin Kim ,&nbsp;Bong-Hwan Choi","doi":"10.1016/j.gene.2025.149956","DOIUrl":"10.1016/j.gene.2025.149956","url":null,"abstract":"<div><div>Korean indigenous goats are maintained as purebred lineages in geographically isolated populations such as Dangjin, Gyeongsang National University (GNU), Jangsu, and Tongyeong. However, their small population size and high rates of inbreeding have raised concerns regarding the preservation of genetic diversity. We generated SNP genotypes for 217 Korean indigenous goats using the GoatSNP50 BeadChip, and standardized body size measurements with complete metadata were available for 64 adult individuals. Principal component analysis (PCA) clearly separated the four lineages, with the GNU population showing particularly high values of inbreeding coefficient and proportion of runs of homozygosity, reflecting the impact of recent closed breeding. Genome-wide patterns of haplotype sharing revealed exploratory trends suggesting that introgression from global breeds tended to coincide with larger body size, whereas intensified inbreeding within the Korean population showed a general tendency toward reduced body size. Furthermore, cross-population extended haplotype homozygosity (XP-EHH) analysis revealed candidate genes, including <em>ADGRL3</em>, <em>SP8</em>, and <em>ARL6IP5</em> that are likely involved in adaptation to seasonal environmental stress. Our findings highlight the global connectivity, functional relevance of body conformation traits, and selective signatures of Korean indigenous goats, providing a genomic foundation for preserving diversity and guiding future breeding.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"980 ","pages":"Article 149956"},"PeriodicalIF":2.4,"publicationDate":"2026-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145752089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Gene therapy for Krabbe disease: evidence from mouse and canine models 克拉伯病的基因治疗:来自小鼠和犬模型的证据。
IF 2.4 3区 生物学
Gene Pub Date : 2026-02-20 Epub Date: 2025-12-09 DOI: 10.1016/j.gene.2025.149949
Yang Li , Xiang Dong , Jian Guo , Ya-feng Lv
{"title":"Gene therapy for Krabbe disease: evidence from mouse and canine models","authors":"Yang Li ,&nbsp;Xiang Dong ,&nbsp;Jian Guo ,&nbsp;Ya-feng Lv","doi":"10.1016/j.gene.2025.149949","DOIUrl":"10.1016/j.gene.2025.149949","url":null,"abstract":"<div><div>Globoid cell leukodystrophy (GLD) is an autosomal recessive lysosomal storage disorder caused by mutations in the β-galactosylceramidase<!--> <!-->(<em>GALC</em>) gene, resulting in enzyme deficiency and the progressive accumulation of galactosylsphingosine and galactosylceramide in the white matter of the central nervous system and in peripheral nerves, which in turn triggers demyelination. Although no curative therapy is currently available, studies in animal models in recent years have shown that gene therapy can ameliorate pathological and biochemical abnormalities and holds considerable promise for clinical translation. This article reviews advances in gene therapy in animal models of GLD and discusses key directions and challenges for future treatments.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"980 ","pages":"Article 149949"},"PeriodicalIF":2.4,"publicationDate":"2026-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145741704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Bioinformatics applications in pharmacogenomics: towards personalized medicine 生物信息学在药物基因组学中的应用:走向个性化医疗
IF 2.4 3区 生物学
Gene Pub Date : 2026-02-10 Epub Date: 2025-12-04 DOI: 10.1016/j.gene.2025.149935
Nabil Zaid , Lamyaa Benchikhi , Banacer Himmi , Hassan Ghazal
{"title":"Bioinformatics applications in pharmacogenomics: towards personalized medicine","authors":"Nabil Zaid ,&nbsp;Lamyaa Benchikhi ,&nbsp;Banacer Himmi ,&nbsp;Hassan Ghazal","doi":"10.1016/j.gene.2025.149935","DOIUrl":"10.1016/j.gene.2025.149935","url":null,"abstract":"<div><div>Pharmacogenomics investigates how genetic variation influences individual responses to drug therapy and aims to optimize treatment outcomes through personalized approaches. Bioinformatics plays a foundational role in this field, enabling the processing, annotation, and interpretation of complex genomic and multi-omics datasets. This review explores the current landscape of bioinformatics in pharmacogenomics, including key databases, variant analysis tools, and artificial intelligence-driven predictive models. It also discusses the integration of multi-omics data, real-world clinical applications, and the regulatory and ethical frameworks supporting clinical implementation. Finally, the role of pharmacogenomics in drug discovery and development is highlighted, illustrating how genetic insights contribute to target identification, trial design, and drug repurposing. Together, these components form the computational backbone of precision medicine and are essential for translating genomic knowledge into actionable, patient-centered care.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"979 ","pages":"Article 149935"},"PeriodicalIF":2.4,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145682437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
DoWRKY26 positively regulating flavonoid biosynthesis in Dendrobium officinale dowky26正调控铁皮石斛类黄酮生物合成。
IF 2.4 3区 生物学
Gene Pub Date : 2026-02-10 Epub Date: 2025-12-06 DOI: 10.1016/j.gene.2025.149944
Ziling Tao , Shiyu Cai , YiMing Wang, Fengxiu li, Lu Lv, Haimeng Bai, Ludan Li, Jihong Jiang, Xiaoying Cao
{"title":"DoWRKY26 positively regulating flavonoid biosynthesis in Dendrobium officinale","authors":"Ziling Tao ,&nbsp;Shiyu Cai ,&nbsp;YiMing Wang,&nbsp;Fengxiu li,&nbsp;Lu Lv,&nbsp;Haimeng Bai,&nbsp;Ludan Li,&nbsp;Jihong Jiang,&nbsp;Xiaoying Cao","doi":"10.1016/j.gene.2025.149944","DOIUrl":"10.1016/j.gene.2025.149944","url":null,"abstract":"<div><div><em>Dendrobium officinale</em> is renowned as the foremost among the “Nine Immortal Herbs of China”. Our previous research showed enhanced flavonoid accumulation following induction by the endophyte <em>Wickerhamomyces</em> sp. KLBMPSYLp8. Transcriptome data analysis identified multiple upregulated transcription factor (TF) genes. We conducted transient overexpression analysis of 10 significantly upregulated TF genes in <em>D. officinale</em> leaves. The results demonstrated that transient overexpression of the <em>DoWRKY26</em> significantly enhanced flavonoid accumulation, with a 33 % increase compared to the empty vector control group. Furthermore, <em>DoWRKY26</em> overexpression also upregulated the expression levels of key enzyme genes implicated in the flavonoid biosynthesis pathway. Subcellular localization confirmed its nuclear presence. <em>DoWRKY26</em> expression was induced by salicylic acid (SA), abscisic acid (ABA), 1-Aminocyclopropane-1-carboxylic Acid (ACC) and methyl jasmonate (MeJA). Yeast one-hybrid (Y1H), Electrophoretic mobility shift assay (EMSA) and dual-luciferase reporter assays verified that DoWRKY26 could bind and activate the promoter of <em>DoCCoAOMT</em>. These findings provide a foundational basis for further exploring the biosynthesis and transcriptional regulation mechanisms of flavonoids in <em>D. officinale</em>.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"979 ","pages":"Article 149944"},"PeriodicalIF":2.4,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145707083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Dynamic tumor microenvironment remodeling from laryngeal leukoplakia to carcinoma revealed by single-cell transcriptomics 单细胞转录组学揭示喉白斑到癌的动态肿瘤微环境重塑。
IF 2.4 3区 生物学
Gene Pub Date : 2026-02-10 Epub Date: 2025-11-23 DOI: 10.1016/j.gene.2025.149917
Yunyi Liu, Peiyun Zhuang
{"title":"Dynamic tumor microenvironment remodeling from laryngeal leukoplakia to carcinoma revealed by single-cell transcriptomics","authors":"Yunyi Liu,&nbsp;Peiyun Zhuang","doi":"10.1016/j.gene.2025.149917","DOIUrl":"10.1016/j.gene.2025.149917","url":null,"abstract":"<div><div>Laryngeal leukoplakia represents the most frequent precancerous lesion in laryngeal carcinogenesis, yet its transformation mechanisms remain elusive. By performing scRNA-seq on ten clinical specimens (five leukoplakia lesions across pathological stages, four early carcinomas, and one control), we established the first single-cell atlas of this malignant progression. Computational analysis revealed dynamic microenvironmental shifts dominated by epithelial cells, fibroblasts, and mononuclear phagocytes. We identified two critical epithelial subpopulations: Epi_4 (tumor-like cells), a high-grade dysplasia-specific subpopulation with high malignant potential, and Epi_5 (tumor cells) in carcinoma, which carries a favorable prognostic gene signature (Module 3). Furthermore, Epi_4 showed preferential communication with cancer-associated fibroblasts (CAFs) and tumor-associated macrophages (TAMs) via the JAG1-NOTCH4 and CXCL5-CXCR1 axes, suggesting actionable therapeutic targets. We also observed the progressive activation of genes involved in redox processes (NQO1, GSTM3, UCHL1, NTRK2) via the KEAP1-NRF2 pathway. This work systematically characterizes the cellular and molecular landscape during laryngeal leukoplakia malignant transformation, providing a framework for future mechanistic studies and early detection strategies.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"979 ","pages":"Article 149917"},"PeriodicalIF":2.4,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145603115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Genetic analysis of a Chinese family with non-syndromic tooth agenesis may reveal a potential multi-locus etiology 对一个中国非综合征性牙齿发育家族的遗传分析可能揭示潜在的多位点病因。
IF 2.4 3区 生物学
Gene Pub Date : 2026-02-10 Epub Date: 2025-11-20 DOI: 10.1016/j.gene.2025.149915
Youmei Wu, Xinzhu Li, Junyang Chen, Bo Yang, Xiaojun Yang, Jin Hou
{"title":"Genetic analysis of a Chinese family with non-syndromic tooth agenesis may reveal a potential multi-locus etiology","authors":"Youmei Wu,&nbsp;Xinzhu Li,&nbsp;Junyang Chen,&nbsp;Bo Yang,&nbsp;Xiaojun Yang,&nbsp;Jin Hou","doi":"10.1016/j.gene.2025.149915","DOIUrl":"10.1016/j.gene.2025.149915","url":null,"abstract":"<div><div>Tooth agenesis (TA), one of the most common craniofacial developmental anomalies, is characterized by the congenital absence of one or more teeth. While numerous genes have been implicated in non-syndromic tooth agenesis (NSTA), its genetic architecture often remains complex. In this study, we investigated the genetic basis of NSTA in a two-generation Chinese family utilizing whole-exome sequencing (WES) complemented by Sanger sequencing. Our analysis revealed a complex segregation pattern of multiple variants. After systematic filtering based on pathogenicity predictions and minor allele frequency (MAF), we identified eight potential contributory variants. These include homozygous missense variants in <em>EDAR</em> (c.1109 T &gt; C), <em>GHR</em> (c.1630A &gt; C), and <em>COL17A1</em> (c.629C &gt; T), a heterozygous missense variant in <em>CEP152</em> (c.161C &gt; T), and <em>DSP</em> (c.5213G &gt; A) and three rare heterozygous missense variants in <em>CCDC154</em> (c.925C &gt; T), <em>FRAS1</em> (c.9628G &gt; A), and <em>NBAS</em> (c.5095G &gt; A). Notably, the variants in <em>GHR</em>, <em>CCDC154</em>, <em>FRAS1</em>, and <em>NBAS</em> represent potential novel candidate genes for NSTA, thereby expanding the variant spectrum associated with this condition. The co-segregation of these multi-locus variants suggests that inheritance<!--> <!-->might<!--> <!-->be complex, perhaps involving oligogenic mechanisms. This<!--> <!-->points to the possibility<!--> <!-->of intricate genetic interactions in tooth development, offering new clues about the molecular basis of familial NSTA.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"979 ","pages":"Article 149915"},"PeriodicalIF":2.4,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145582018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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