Gene最新文献

{"title":"Pugionium cornutum PcHARBI1-5 (Harbinger Transposase Derived 1–5) facilitates early flowing and seed development in in Arabidopsis thaliana","authors":"Yunwei Zhao,&nbsp;Kaifan Shang,&nbsp;Ping Wang","doi":"10.1016/j.gene.2025.149914","DOIUrl":"10.1016/j.gene.2025.149914","url":null,"abstract":"<div><div><em>Pugionium cornutum</em> is a biennial herb belonging to the Brassicaceae family and is an endemic species of the Mongolian Plateau, exhibiting strong stress tolerance and notable medicinal value. In this study, the <em>PcHARBI1-5</em> gene was cloned from <em>P. cornutum</em> and functionally characterized through heterologous transformation in <em>Arabidopsis thaliana</em>. Transgenic overexpression lines (OE) and homologous knockout mutants (KO-1) were generated, and their phenotypic differences were systematically evaluated under controlled conditions. Overexpression of <em>PcHARBI1-5</em> significantly promoted early flowering in <em>Arabidopsis</em>, with transgenic plants flowering approximately four days earlier than wild-type controls, whereas the KO-1 mutant exhibited a delay of about three days. Furthermore, transgenic lines displayed enhanced agronomic performance, including longer roots, increased plant height, greater lateral branching, elongated siliques, and higher seed yield per plant. Gene expression analysis revealed that <em>PcHARBI1-5</em> modulates flowering time by down-regulating the floral repressor <em>FLC</em> and up-regulating key floral integrators <em>FT</em> and <em>SOC1</em>. Taken together, this study reports the successful cloning and functional validation of <em>PcHARBI1-5</em> from <em>P. cornutum</em>, demonstrating its pivotal role in accelerating flowering and improving multiple agronomic traits. These findings highlight <em>PcHARBI1-5</em> as a promising candidate gene for molecular breeding strategies aimed at developing early-maturing and high-yielding crop varieties.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"978 ","pages":"Article 149914"},"PeriodicalIF":2.4,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145577704","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}

{"title":"Characterization of the gut microbiota in patients with stage III colorectal cancer: A case-control study","authors":"Mahamane T. Diakité ,&nbsp;Shan Sun ,&nbsp;Anou M. Somboro ,&nbsp;Brehima Diakité ,&nbsp;Amadou Koné ,&nbsp;Yaya Kassogué ,&nbsp;Djeneba Fofana ,&nbsp;Saidou Balam ,&nbsp;Cheick B Traoré ,&nbsp;Aminata Maiga ,&nbsp;Bakarou Kamaté ,&nbsp;Djibril Ba ,&nbsp;Modibo Diarra ,&nbsp;Soungou Boré ,&nbsp;Almoustapha I. Maiga ,&nbsp;Qi Dai ,&nbsp;Drew Robert Nannini ,&nbsp;Jane Holl ,&nbsp;Robert Murphy ,&nbsp;Lifang Hou ,&nbsp;Mamoudou Maiga","doi":"10.1016/j.gene.2025.149913","DOIUrl":"10.1016/j.gene.2025.149913","url":null,"abstract":"<div><h3>Aim</h3><div>To conduct a case-control study (pilot study) in Africa (Mali) in comparing the gut microbiota of patients with stage III colorectal cancer (CRC) using next-generation sequencing.</div></div><div><h3>Methods</h3><div>Shotgun sequencing was performed to characterize participants’ fecal microbiota using Illumina’s HiSeq platform. This case-control study involved newly diagnosed CRC patients (n = 23) prior to any treatment initiation, and unrelated healthy controls (n = 24) to elucidate their microbial diversity and relative abundance.</div></div><div><h3>Results</h3><div>The findings revealed that the gut microbiota in CRC and in healthy were significantly distinctive according to the PERMANOVA test (R² = 0.132, P = 0.001), and the alpha-diversity was significantly lower in CRC. Beta-diversity, based on principal coordinate analysis, showed a distinct taxonomy between the CRC and the healthy.</div><div>Levels of <em>Pseudomonadota</em>, <em>Escherichia</em>, <em>Citrobacter freundii</em>, <em>Klebsiella</em> sp. <em>LTGPAF-6F</em>, <em>Escherichia albertii, Escherichia coli, Caudovirales</em>, <em>Apicomplexa,</em> and <em>Verrucomicrobiota</em> populations were significantly elevated in CRC. The major metabolic pathways with higher relative abundance levels found in CRC compared to healthy were related to <em>HEMESYN2-PWY: heme biosynthesis II (anaerobic)</em>, <em>PWY-5154:L-arginine biosynthesis III (via N-acetyl-L-citrulline)</em>, <em>FUC-RHAMCAT-PWY: superpathway of fucose and rhamnose degradation</em>, <em>ECASYN-PWY: enterobacterial common antigen biosynthesis, ENTBACSYN-PWY: enterobactin biosynthesis,</em> and <em>AEROBACTINSYN-PWY: aerobactin biosynthesis.</em></div></div><div><h3>Conclusion</h3><div>Distinct gut microbiome profiles between healthy and CRC were observed. In particular, the findings showed a significant reduction in microbial diversity in stage III CRC. This study provides initial metagenomic data on Malian patients with CRC. It will be used to create a larger cohort to better understand the relationship between CRC and the gut microbiota in the Malian CRC population.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"978 ","pages":"Article 149913"},"PeriodicalIF":2.4,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145573420","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}

{"title":"Retraction notice to “Genetic variations of prostate stem cell antigen (PSCA) contribute to the risk of gastric cancer for Eastern Asians: a Meta-analysis based on 16792 individuals”. [Gene 493 (2012) 83–91]","authors":"Lei Qiao,&nbsp;Yong Feng","doi":"10.1016/j.gene.2025.149823","DOIUrl":"10.1016/j.gene.2025.149823","url":null,"abstract":"","PeriodicalId":12499,"journal":{"name":"Gene","volume":"976 ","pages":"Article 149823"},"PeriodicalIF":2.4,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145548980","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}

{"title":"De novo PKD1 splicing and missense variants in two familial ADPKD: Molecular characterization and genetic counseling implications","authors":"Juan Zhu ,&nbsp;Zi-yan Xu ,&nbsp;Hong-ping Yu ,&nbsp;Ruo-li Wang ,&nbsp;Yi-jia Luo ,&nbsp;Li-jun Xie ,&nbsp;Jian-hui Zhang ,&nbsp;Qian Chen ,&nbsp;Peng-fei Wang ,&nbsp;Dan-dan Ruan ,&nbsp;Jing Zou ,&nbsp;Yan-feng Zhou ,&nbsp;Li Chen ,&nbsp;Fang-meng Huang ,&nbsp;Mei-zhu Gao ,&nbsp;Li Zhang ,&nbsp;Yun-fei Li ,&nbsp;Zhu-ting Fang ,&nbsp;Li-sheng Liao ,&nbsp;Xi-kui Zhang ,&nbsp;Zhi-hai Zheng","doi":"10.1016/j.gene.2025.149902","DOIUrl":"10.1016/j.gene.2025.149902","url":null,"abstract":"<div><div>This study identifies two pedigrees with autosomal dominant polycystic kidney disease (ADPKD) caused by de novo PKD1 variants. Proband A carried a heterozygous splicing variant (c.9202-16G &gt; A), presenting with bilateral renal cysts. The miniGENE assay confirmed this variant causes aberrant splicing with a 60-base excision, leading to a frameshift and a predicted truncated protein. Proband B carried a missense variant (c.2180 T &gt; C; p.Leu727Pro), presenting with polycystic kidney and liver disease. Structural modeling revealed this variant severely disrupts local secondary structure and a critical spatial interaction, compromising protein stability. Functional analyses demonstrate that both de novo variants are pathogenic through distinct mechanisms, implicating aberrant splicing and structural disruption in ADPKD etiology.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"978 ","pages":"Article 149902"},"PeriodicalIF":2.4,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145534407","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}

{"title":"ContigPolishing: A User-Friendly Java GUI for contig extension and refinement in prokaryotic genomes","authors":"Rosyely da Silva Oliveira ,&nbsp;Nilson César Oliveira Alves Filho ,&nbsp;Walter de Barros Gomes Netto ,&nbsp;Denis de Castro Silva ,&nbsp;Mônica Silva de Oliveira ,&nbsp;Ana Carolina Favacho Miranda de Oliveira ,&nbsp;Rafael Azevedo Baraúna ,&nbsp;Diego Assis das Graças ,&nbsp;Artur Silva ,&nbsp;Adonney Allan de Oliveira Veras","doi":"10.1016/j.gene.2025.149893","DOIUrl":"10.1016/j.gene.2025.149893","url":null,"abstract":"<div><div>To determine the gene content of an organism, the reads generated by the sequencing process must be assembled using an assembly strategy, either by reference or de novo. However, this process often results in multiple sequences called contigs, which, after the sorting steps, are grouped into scaffolds. The completion stage aims to obtain a single genomic sequence, called a complete genome, which is not a trivial task. Various analytical strategies have been developed to help in this process, many of which have been implemented in computer tools to obtain complete genomes or as close to this as possible, the so-called drafts. The manuscript presents ContigPolishing, a computational tool with a simple and intuitive graphical interface, developed to improve the assembly of prokaryotic genomes, such as bacteria and metagenomes. Despite existing software, there is a gap for solutions that combine simplicity and robustness. ContigPolishing addresses this need, featuring an integrated database that allows processing to be resumed at any time. The tool was validated with 90 NCBI datasets from genera such as Escherichia coli, Corynebacterium, and Nocardia, as well as raw reads from the SRA database to simulate real-world situations. The results showed improvement in the contiguity of the assemblies, with an increase in N50 and improvement in L50, and a reduction in the number of contigs, by extending the contigs using the similarity between their flanks. In some cases, the software was able to elevate the status of genomes from draft to complete, proving its efficiency. ContigPolishing is available at: <span><span>https://github.com/allanverasce/contigpolishing</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"979 ","pages":"Article 149893"},"PeriodicalIF":2.4,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145523192","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}

{"title":"Combined genomic profiling by exome sequencing analysis and optical genome mapping reveals bi-allelic somatic inactivation of SMAD4 in pediatric colon adenocarcinoma","authors":"Mari C. Morán-Espinosa ,&nbsp;Aldo Zaragoza-Fernández ,&nbsp;Karem Yohaly Pérez-López ,&nbsp;Cristian Jesús Huchim-Peña ,&nbsp;Pedro Velarde-Hernández ,&nbsp;María Argelia Escobar-Sánchez ,&nbsp;Rodrigo Moreno-Salgado ,&nbsp;Rocío Sánchez-Urbina ,&nbsp;Hector Diaz-Garcia ,&nbsp;Guillermo Aquino Jarquin ,&nbsp;Javier T. Granados-Riverón","doi":"10.1016/j.gene.2025.149891","DOIUrl":"10.1016/j.gene.2025.149891","url":null,"abstract":"","PeriodicalId":12499,"journal":{"name":"Gene","volume":"978 ","pages":"Article 149891"},"PeriodicalIF":2.4,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145523202","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}

{"title":"Genetic diversity, natural selection, and immunological features of the Plasmodium vivax CyRPA protein: Implications for vaccine development","authors":"Diego Garzón-Ospina ,&nbsp;Sindy P. Buitrago ,&nbsp;Natalia Cepeda-Riaño ,&nbsp;Carlos J. Castro-Cavadía ,&nbsp;María Fernanda Yasnot-Acosta","doi":"10.1016/j.gene.2025.149894","DOIUrl":"10.1016/j.gene.2025.149894","url":null,"abstract":"<div><div>Malaria caused by <em>Plasmodium vivax</em> remains a significant public health challenge, with vaccine development hindered by factors such as antigenic diversity and immune evasion. The Cysteine-Rich Protective Antigen (CyRPA), a key protein involved in erythrocyte invasion, has emerged as a promising vaccine candidate. However, its genetic diversity and immunological properties have not been fully explored. This study aimed to analyze the genetic diversity, selective pressures, and antigenic potential of the <em>pvcyrpa</em> locus using 950 sequences, including 42 newly obtained isolates from Colombia. The <em>pvcyrpa</em> gene displayed high nucleotide diversity shaped by both natural selection and recombination. <em>In-silico</em> predictions identified B- and T-cell epitopes, encompassing mainly polymorphic regions, with strong binding affinities predicted for multiple HLA alleles. Notably, these epitopes overlapped with regions previously shown to elicit immune responses in natural infections, as reported in a recent study. Moreover, immune simulation of a multiepitope C-terminal construct predicted a robust humoral memory profile. Collectively, these genetic, epitope-mapping, and immune-simulation findings highlight the conserved C-terminal region of PvCyRPA as a strong, broadly reactive vaccine candidate, providing a rational basis for subsequent <em>in-vitro</em> and <em>in-vivo</em> validation.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"978 ","pages":"Article 149894"},"PeriodicalIF":2.4,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145523126","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}

{"title":"Retraction notice to “Association between -251A> T polymorphism in the interleukin-8 gene and oral cancer risk: a meta-analysis.” [Gene 522 (2013) 168–176]","authors":"Zhiming Wang,&nbsp;Chuanning Wang,&nbsp;Zhiguo Zhao,&nbsp;Fang Liu,&nbsp;Xinming Guan,&nbsp;Xiaoping Lin,&nbsp;Liping Zhang","doi":"10.1016/j.gene.2025.149875","DOIUrl":"10.1016/j.gene.2025.149875","url":null,"abstract":"","PeriodicalId":12499,"journal":{"name":"Gene","volume":"975 ","pages":"Article 149875"},"PeriodicalIF":2.4,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145503308","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}

{"title":"Mettl1 mitigates sepsis-induced cardiomyopathy via inhibition of FDX1-dependent cuproptosis","authors":"Wei Siang ,&nbsp;Wang Guoyun ,&nbsp;Feng Yan ,&nbsp;Lin Wenji","doi":"10.1016/j.gene.2025.149892","DOIUrl":"10.1016/j.gene.2025.149892","url":null,"abstract":"<div><div>Sepsis-induced cardiomyopathy (SICM) significantly contributes to sepsis-related mortality, yet its molecular mechanisms remain incompletely understood. Here, we identify cuproptosis—a copper-dependent mitochondrial cell death pathway—as a critical driver of SICM pathogenesis. In a murine SICM model induced by lipopolysaccharide (LPS), cardiac dysfunction was accompanied by myocardial copper accumulation and dysregulation of cuproptosis regulators. RNA sequencing (RNA-seq) analysis revealed cuproptosis as one of the top enriched pathways. Crucially, we demonstrate that the m7G methyltransferase Mettl1 functions as a cardioprotective factor. Mettl1 expression was upregulated in septic hearts and positively correlated with copper levels. <em>In vitro</em>, Mettl1 knockdown exacerbated LPS-induced cytotoxicity in cardiomyocytes and amplified intracellular copper overload. Mechanistically, Mettl1 deficiency potentiated LPS-triggered upregulation of FDX1—a key executor of cuproptosis—and suppressed PDHA1 expression. Our findings establish Mettl1 as a novel suppressor of cuproptosis that confers protection against sepsis-induced cardiotoxicity by restraining FDX1-mediated copper-dependent cell death. Targeting the Mettl1-FDX1 axis may offer a promising therapeutic strategy for SICM.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"978 ","pages":"Article 149892"},"PeriodicalIF":2.4,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145511585","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}

{"title":"β-catenin/TCF4/NANOG axis controls miR-302 transcription in colorectal cancer cells","authors":"Kiarash Saleki ,&nbsp;Miao Xue ,&nbsp;Amirreza Mazloomi ,&nbsp;Bradley Spencer-Dene ,&nbsp;Abdolrahman S. Nateri","doi":"10.1016/j.gene.2025.149890","DOIUrl":"10.1016/j.gene.2025.149890","url":null,"abstract":"<div><div>The miR-302 cluster, a key pluripotency-associated non-coding RNA, has been implicated in stem cell homeostasis and tumourigenesis. However, its regulatory mechanisms in cancers, including colorectal cancer (CRC) remain poorly understood. Here, we demonstrate that the β-catenin/TCF4 complex significantly enhances miR-302 expression through direct promoter activation in CRC cells. We hypothesized that the β-catenin/TCF4 complex directly activates the miR-302 promoter and cooperates with NANOG in a transcriptional feedback loop sustaining stem-like traits in CRC cells. Using a combination of promoter-driven luciferase reporter assays, chromatin immunoprecipitation (ChIP), and molecular dynamics simulations, we identify a regulatory axis involving Wnt signalling and the transcription factor NANOG. Our data show that individual members of the miR-302 cluster activate the NANOG promoter, while both NANOG and β-catenin/TCF4 synergistically enhance miR-302 promoter activity, suggesting the presence of a positive feedback loop. Structural simulations further elucidate the binding interactions between TCF4, NANOG, and the miR-302 promoter, corroborating our experimental observations. Together, these findings position miR-302 as a downstream effector of Wnt/β-catenin signalling and an integral component of NANOG-mediated transcriptional networks in CRC stem-like cells. This work advances our understanding of non-coding RNA regulation in cancer and highlights potential therapeutic opportunities for targeting stemness-associated pathways.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"977 ","pages":"Article 149890"},"PeriodicalIF":2.4,"publicationDate":"2025-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145503311","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}