Gene最新文献

{"title":"ActO, a positive cluster-situated regulator for actinomycins biosynthesis in Streptomyces antibioticus ZS","authors":"","doi":"10.1016/j.gene.2024.148962","DOIUrl":"10.1016/j.gene.2024.148962","url":null,"abstract":"<div><div>Actinomycins are a class of cyclic lipopeptide antibiotics produced by <em>Streptomyces</em>, which have rich biological activities and demonstrate great potential value. Among them, actinomycin D is currently the effective drug for some malignant tumor diseases. Although the chemical properties, biological activities and biosynthesis of actinomycins have been extensively studied, the regulation of their biosynthesis remains poorly understood. <em>Streptomyces antibioticus</em> ZS isolated from deep-sea corals is a producer of actinomycin D and actinomycin V. Here, we reported the characterization of a cluster-situated regulator ActO in actinomycins biosynthetic gene cluster (<em>act</em> cluster) of <em>S. antibioticus</em> ZS, which belongs to LmbU family. Deletion of <em>actO</em> completely blocked the synthesis of actinomycins. Overexpression of <em>actO</em> increased the yields of actinomycin D and actinomycin V by 4.4 fold and 2.6 fold, respectively. The result of RT-qPCR showed that ActO activates the transcription of all genes in <em>act</em> cluster. However, no specific binding of His₆-ActO to the promoters of target genes was observed after electrophoretic mobility shift assay (EMSA). These results proved that ActO serves as a positive regulator involved in the biosynthesis of actinomycins, affecting the transcription of all genes related to the synthesis of intermediates, skeleton modification and extracellular transportation of final products. Moreover, we demonstrated that overexpression of <em>actO</em> is a novel strategy to increase the yields of actinomycins.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142322155","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":"Transcriptome analysis unveils PLSCR1 associated with microglial polarization in neuropathic pain","authors":"","doi":"10.1016/j.gene.2024.148961","DOIUrl":"10.1016/j.gene.2024.148961","url":null,"abstract":"<div><div>Neuropathic pain (NP) continues to be a significant problem that lacks effective treatment. Our study sought to explore a new promising gene target for the treatment of NP. Differential and enrichment analyses were performed on 24,197 genes and 12,088 genes from the NP microglial microarray and sequencing dataset. Candidate differentially expressed genes (DEGs), functions, and signaling pathways that are closely related to NP were identified by analyzing the bioinformatic results. For <em>in vivo</em> experiments, mice were divided into the sham and NP groups. The expressions of DEGs were validated to screen out the NP hub genes. For <em>in vitro</em> experiments, the hub genes in resting M0-BV2 and polarized M1-BV2 microglia were examined by immunofluorescence, flow cytometry, and qRT-PCR. DEGs in the NP microarray and sequencing data shared five candidate genes, CD244, MEGF9, PCGF2, PLSCR1, and NECAB2. The results of the <em>in vivo</em> experiment showed that the NP model group exhibited higher expression of PLSCR1 and MEGF9 compared to the sham group. The enrichment results of the DEGs revealed the biological processes of “response to lipopolysaccharide”. PLSCR1 was highly expressed in the lipopolysaccharide-induced M1-BV2 microglia. PLSCR1 is a potential gene associated with microglial polarization in NP. These findings provide a new view on understanding the pathogenesis mechanism of NP.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0378111924008424/pdfft?md5=4f45cfb88d1513c741b87f175b168812&pid=1-s2.0-S0378111924008424-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142307492","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":"Chromoanagenesis of chromosome 22 in a subject with obesity and borderline cognitive performance","authors":"","doi":"10.1016/j.gene.2024.148956","DOIUrl":"10.1016/j.gene.2024.148956","url":null,"abstract":"<div><div>Chromoanagenesis events consist of complex chromosome rearrangements with multiple breakpoints in one or few chromosomes. Mechanisms of chromoanagenesis are split into three major groups: chromothripsis, chromoanasynthesis and chromoplexy. This study aims to delineate a chromoanagenesis event at the level of chromosome 22 in an individual showing obesity and borderline cognitive performance as major disturbances. The proband and his parents were subjected to conventional karyotyping, CGH array and whole genomic sequencing (WGS). By conventional karyotyping a “de novo” pericentric inversion of chromosome 22 was identified. CGH array identified several imbalances (either deletions or duplications) in the long arm of chromosome 22; the largest is a 4.5 Mb duplication at 22q12.1-22q1.3. The detection of extensive duplications would suggest the occurrence of a chromoanasynthesis event. WGS, in addition to the structural alterations identified by karyotyping and CGH array, revealed two translocations from chromosome 22 to chromosomes 6 and 21 as well as a heterozygous pathogenetic variant of <em>ALMS1</em> gene; the latter could have contributed to the obesity of our patient. The pericentric inversion induces loss of initial part of <em>TCF20</em> gene including the 5’ regulatory region and the first, noncoding, exon. Heterozygous loss-of-function mutations of <em>TCF20</em> gene have been found in patients with autism spectrum disorder or intellectual disability, some of them presenting obesity. It is, therefore, possible that disruption of <em>TCF20</em> gene structure would contribute to a fraction of the patient’s phenotype.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142307490","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":"Integrated GMPS and RAMP3 as a signature to predict prognosis and immune heterogeneity in hepatocellular carcinoma","authors":"","doi":"10.1016/j.gene.2024.148958","DOIUrl":"10.1016/j.gene.2024.148958","url":null,"abstract":"<div><h3>Background</h3><div>Hepatocellular carcinoma (HCC) is a highly fatal malignant worldwide. As different expression levels of specific genes can lead to different HCC outcomes, we aimed to develop a gene signature capable of predicting HCC prognosis.</div></div><div><h3>Methods</h3><div>In this study, transcriptomic sequencing and relevant clinical data were extracted from public platforms. The guanine monophosphate synthase (GMPS)|receptor activity-modifying protein 3 (RAMP3) gene pair was developed based on the relative values of gene expression levels. Nomograms were developed using R software. Immune status was assessed through single‐sample gene set enrichment analysis. GMPS knockdown was achieved through siRNA transfection. Quantitative reverse transcription PCR, apoptosis assays, and cell proliferation were performed to verify the function of GMPS|RAMP3 in HCC cells.</div></div><div><h3>Results</h3><div>Here, a gene pair containing GMPS and RAMP3 was successfully constructed. We demonstrated that the GMPS|RAMP3 gene pair was an independent predictor with strong prognostic prediction power, based on which a nomogram was established. Functional analysis revealed that the enrichment of cell cycle-related pathways and immune status differed considerably between the two groups, with cell cycle-related genes highly expressed in the high GMPS|RAMP3 value group. Finally, cell experiments indicated that GMPS knockdown significantly repressed proliferation, promoted apoptosis, and enhanced the sensitivity of HCC cells to gemcitabine.</div></div><div><h3>Conclusions</h3><div>The gene pair GMPS|RAMP3 is a novel prognostic predictor of HCC, providing a promising approach to the treatment and assessment of immune heterogeneity in HCC.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142307491","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":"Erratum to \"tRNA-derived RNA fragment, tRF-18-8R6546D2, promotes pancreatic adenocarcinoma progression by directly targeting ASCL2\" [GENE 927C (2024) 148739].","authors":"Sihua Lan, Sixue Liu, Ke Wang, Wenying Chen, Dandan Zheng, Yanyan Zhuang, Shineng Zhang","doi":"10.1016/j.gene.2024.148909","DOIUrl":"https://doi.org/10.1016/j.gene.2024.148909","url":null,"abstract":"","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142283599","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":"Corrigendum to \"Multilocus functional characterization of indigenous and exotic inbreds for dgat1-2, fatb, ge2 and wri1a genes affecting kernel oil and fatty acid profile in maize\" [Gene 895 (2024) 148001].","authors":"Ashvinkumar Katral, Firoz Hossain, Rajkumar U Zunjare, Rashmi Chhabra, T Vinutha, Hriipulou Duo, Bhupender Kumar, Chikkappa G Karjagi, Sherry R Jacob, Sushil Pandey, Chirravuri N Neeraja, Sujata Vasudev, Vignesh Muthusamy","doi":"10.1016/j.gene.2024.148950","DOIUrl":"https://doi.org/10.1016/j.gene.2024.148950","url":null,"abstract":"","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142283597","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 complete mitochondrial genomes of four tarantulas (Arachnida: Theraphosidae) with phylogenetic analysis","authors":"","doi":"10.1016/j.gene.2024.148954","DOIUrl":"10.1016/j.gene.2024.148954","url":null,"abstract":"<div><div>To better understand the evolution of mitochondrial genomes (mitogenomes) within the family Theraphosidae, we characterized mitogenomes of four tarantulas (<em>Grammostola pulchripes</em>, <em>Phormictopus atrichomatus</em>, <em>Pterinochilus murinus</em> and <em>Pterinopelma sazimai</em>) for the first time. The mitogenomes were all classical circular structures, with lengths ranging from 13,822 bp to 14,011 bp. The constitutive genes and the orientation of the coding strand observed in the four mitogenomes were consistent with those found in other species belonging to the Theraphosidae family. The four mitogenomes were compacted and exhibited a preference for A and T, with the rRNA sequences showing a higher A+T content. Ka/Ks and p-distances analyses showed the <em>ND6</em> gene had highest evolutionary rate, while the <em>COⅠ</em> gene displayed relatively slower evolution. In contrast to previous phylogenetic studies, our phylogenetic analysis based on mitogenomes provides new phylogenetic relationships among subfamilies. Subfamily Theraphosinae is most closely related to Ornithoctoninae, slightly distant from Harpactirinae, and farthest from Selenocosmiinae. The new data we acquired regarding these mitogenomes will aid in understanding the complex interrelationships among species within the Theraphosidae family.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142283504","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":"Whole genome re-sequencing reveals high altitude adaptation signatures and admixture in Ladakhi cattle.","authors":"Subrata Koloi, Indrajit Ganguly, Sanjeev Singh, Satpal Dixit","doi":"10.1016/j.gene.2024.148957","DOIUrl":"https://doi.org/10.1016/j.gene.2024.148957","url":null,"abstract":"<p><p>Ladakhi cattle, native to the high-altitude region of Ladakh in northern India (ranging from 3,000 to 5,000 m above sea level), have evolved unique genetic adaptations to thrive in harsh environmental conditions, such as hypoxia, extreme cold, and low humidity. This study explored the genome of Ladakhi cattle to investigate genetic structure, selection signatures, and adaptive mechanisms. Whole genome sequencing reads, generated on Illumina NovaSeq 6000 platform, were aligned to the Bos taurus reference genome with BWA-MEM. SNPs were identified and filtered using GATK and bcftools, and functionally annotated with SnpEff. For population genomic analysis, PCA and admixture modeling assessed genetic structure, while Neighbor-Joining trees, LD decay, nucleotide diversity (π), and FST evaluated phylogenetic relationships and genetic variation. Selective sweeps were detected using RAiSD, and gene-set enrichment and protein-protein interaction analyses were conducted to explore functional pathways related to adaptation. The study revealed 3,759,279 unique SNPs and demonstrated that Ladakhi cattle form a distinct genetic cluster with an estimated admixture of 68 % Bos indicus and 32 % Bos taurus ancestry. Key findings include rapid linkage disequilibrium decay, low inbreeding level, and the identification of selection signatures and genes associated with hypoxia response, energy metabolism, and cold adaptation. Mean nucleotide diversity (π, 0.0037) and FST values indicated moderate genetic differentiation from other breeds. The analysis highlighted selection signatures for genes like HIF1A, ENO4, ANGPT1, EPO, NOS3, MAPK3, HMOX1, BCL2,CAMK2D, MTOR, AKT2,PIK3CB, and MAP2K1, among others, including various keratin and heat shock proteins. The interaction between genes associated with hypoxia signaling (HIF-1) and other enriched pathways such as PI3K, mTOR, NFκB, ERK, and ER stress, reveals a complex mechanism for managing hypoxic stress in Ladakhi cattle. These findings offer valuable insights for breeding programs aimed at enhancing livestock resilience in extreme environments and enhance understanding of mammalian adaptation to high-altitude conditions.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142283601","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":"Deciphering the influence of AP1M2 in modulating hepatocellular carcinoma growth and Mobility through JNK/ErK signaling pathway control.","authors":"Huan Wang, Xin Xie, Minwei Du, Xintong Wang, Kunyuan Wang, Xingyuan Chen, Hui Yang","doi":"10.1016/j.gene.2024.148955","DOIUrl":"https://doi.org/10.1016/j.gene.2024.148955","url":null,"abstract":"<p><strong>Background: </strong>Hepatocellular Carcinoma (HCC) is the most common digestive system malignancy, with unclear pathogenesis and low survival rates. AP1M2 is associated with tumor progression, but its role and molecular mechanisms in HCC remain poorly understood and require further investigation.</p><p><strong>Methods: </strong>We utilized the Gene Expression Omnibus (GEO) and Expression Analysis Interactive Hub (XENA) databases to assess AP1M2 mRNA expression levels in HCC patients. Additionally, we employed the Cancer Genome Atlas (TCGA) database to identify pathways associated with both AP1M2 and HCC development. To evaluate the effect of AP1M2 on HCC cell proliferation and migration, we employed various techniques including EdU, CCK-8, Colony formation assay, and Transwell assays. Furthermore, Western blot analysis was conducted to examine the signaling pathways influenced by AP1M2.</p><p><strong>Results: </strong>AP1M2 expression was significantly increased at the mRNA level in HCC tissues(P<0.001). Importantly, overall survival (OS) analysis confirmed the association between higher AP1M2 expression and a poorer prognosis in HCC patients compared to those with lower AP1M2 expression (P<0.019).Multivariate Cox regression analysis showed that AP1M2 was an independent prognostic factor and a valid predictor for HCC patients. Furthermore, GSEA results indicated differential enrichment of lipid, metal metabolism, and coagulation processes in HCC samples demonstrating a high AP1M2 expression phenotype. In vitro experiments supported these findings by demonstrating that AP1M2 promotes HCC cell proliferation and migration, while activating the JNK/ERK pathway.</p><p><strong>Conclusion: </strong>Our findings indicate that AP1M2 expression may serve as a potential molecular marker indicating a poor prognosis for HCC patients. Furthermore, we have demonstrated that AP1M2 significantly influences HCC cell proliferation and migration, with the JNK/ERK signaling pathway playing a key role in AP1M2-mediated regulation in the context of HCC.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142283598","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":"Increasing prostate cancer radiosensitivity by miR-7-5p knockdown of anti-apoptotic genes","authors":"","doi":"10.1016/j.gene.2024.148951","DOIUrl":"10.1016/j.gene.2024.148951","url":null,"abstract":"<div><p>Despite the success of radiotherapy for prostate cancer treatment, the recent discovery of radiation resistance prevents it from reaching its full potential. This study aims to use hsa-miR-7-5p for the expression of anti-apoptotic genes. The search for anti-apoptotic genes was carried out through databases. The selected genes included XIAP, MCL1, REL, and BIRC3. Our selection was based on the best miRNA because it has a greater impact on genes. The second step involved transfecting the miRNA into a prostate cancer cell line. Subsequently, radiosensitivity was tested using real-time PCR, clonogenic assay, and annexin V flow cytometry. The highest apoptosis rate in the transfected cells was at 0 Gy in hsa-miR-7-5p (28.88 ± 0.80), plenti III (18.81 ± 0.59), and the control group (4.10 ± 1.52) (P&lt;0.001). Also, its rate was at 4 Gy in hsa-miR-7-5p (36.11 ± 1.93), plenti III (26.42 ± 0.42), and the control group (8.79 ± 2.29) (P&lt;0.001). This study showed a decreasing trend in survival with increasing doses. Suppression of anti-apoptotic genes, including XIAP, MCL1, Birc3, and REL, enhanced radiosensitivity by increasing the expression of hsa-miR-7-5p in the PC3 and LNCaP cell lines. Hsa-miR-7-5p is a miRNA that can suppress the expression of anti-apoptotic genes and thus plays an essential role in the process of cell apoptosis. Targeting genes that are associated with apoptosis could potentially enhance the efficacy of treatments for patients with prostate cancer.</p></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142270822","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}