Gene最新文献

{"title":"Micropeptides derived from long non-coding RNAs: Computational analysis and functional roles in breast cancer and other diseases","authors":"Saisai Chen ,&nbsp;Mengru Liu ,&nbsp;Weizhen Yi ,&nbsp;Huagang Li ,&nbsp;Qingsheng Yu","doi":"10.1016/j.gene.2024.149019","DOIUrl":"10.1016/j.gene.2024.149019","url":null,"abstract":"<div><div>Long non-coding RNAs (lncRNAs), once thought to be mere transcriptional noise, are now revealing a hidden code. Recent advancements like ribosome sequencing have unveiled that many lncRNAs harbor small open reading frames and can potentially encode functional micropeptides. Emerging research suggests these micropeptides, not the lncRNAs themselves, play crucial roles in regulating homeostasis, inflammation, metabolism, and especially in breast cancer progression. This review delves into the rapidly evolving computational tools used to predict and validate lncRNA-encoded micropeptides. We then explore the diverse functions and mechanisms of action of these micropeptides in breast cancer pathogenesis, with a focus on their roles in various species. Ultimately, this review aims to illuminate the functional landscape of lncRNA-encoded micropeptides and their potential as therapeutic targets in cancer.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498370","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":"Wnt5a negatively regulates melanogenesis in primary Arctic fox epidermal melanocytes","authors":"Zhilin Hong,&nbsp;Dongxian Wang,&nbsp;Xian Qiao,&nbsp;Yuchun Xie,&nbsp;Shanshan Yang,&nbsp;Kexing Hao,&nbsp;Cong Han,&nbsp;Huayun Liu,&nbsp;Zhengzhu Liu","doi":"10.1016/j.gene.2024.149045","DOIUrl":"10.1016/j.gene.2024.149045","url":null,"abstract":"<div><div>Melanocytes, which are mainly found in the epidermis, are responsible for the melanin of skin and hair, and thereby contribute to the appearance of skin and provide protection from damage by ultraviolet radiation. Our previous study revealed that the <em>Wnt5a</em>, one of the many genes that affect melanin production, might be involved in the coat color seasonal change of the Arctic fox by influencing skin melanogenesis. Although the role of <em>Wnt5a</em> in melanocyte lines and melanoma cells has been extensively studied, its role in primary epidermal melanocytes has not been explored. This study aimed to investigate the role and mechanism of the <em>Wnt5a</em> in influencing melanogenesis in Arctic fox primary epidermal melanocytes. We constructed the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) knockout plasmid targeting exons of the <em>Wnt5a</em> and transfected it into primary epidermal melanocytes. The results of the amplification knockout region assay, RT-qPCR assay, and western blot assay showed the success of <em>Wnt5a</em> knockout. RT-qPCR assay and melanin content assay showed that melanin production in melanocytes was significantly increased after <em>Wnt5a</em> knockout, and melanin-related key genes, such as microphthalmia-associated transcription factor, tyrosinase and tyrosinase-related protein 1, were significantly elevated. In addition, we also found that the expression of the <em>β-catenin</em> gene of the Wnt canonical pathway was significantly elevated after <em>Wnt5a</em> knockout. In conclusion, our results indicate that the <em>Wnt5a</em> plays a negative regulatory role in melanogenesis in primary epidermal melanocytes, and is presumably involved in antagonizing or inhibiting canonical Wnt signaling.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498374","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 \"Dysregulation of deubiquitination in breast cancer\" [Gene (2024) 148175].","authors":"Lili Kong, Xiaofeng Jin","doi":"10.1016/j.gene.2024.149023","DOIUrl":"https://doi.org/10.1016/j.gene.2024.149023","url":null,"abstract":"","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498271","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":"Identification of the mutations in BTD gene in Iranian patients with biotinidase deficiency and evaluating their genotype-phenotype correlations","authors":"Fatemeh Azizinejad ,&nbsp;Majid Aminzadeh ,&nbsp;Maryam Tahmasebi-Birgani ,&nbsp;Solmaz Heidari ,&nbsp;Pegah Ghandil","doi":"10.1016/j.gene.2024.149020","DOIUrl":"10.1016/j.gene.2024.149020","url":null,"abstract":"<div><h3>Background</h3><div>Biotinidase (BTD, encoded by the <em>BTD</em> gene) deficiency is an autosomal recessive neurometabolic disease caused by abnormal BTD activity in the biotin cycle<strong>.</strong> The clinical symptoms of patients, which are mainly neurocutaneous, range from mild to severe based on the enzyme activity level. This study aimed to identify <em>BTD</em> gene mutations in suspected BTD deficiency patients for the first time in the southwest of Iran and evaluate their genotype-phenotype correlations.</div></div><div><h3>Methods</h3><div>11 clinically and biochemically suspected patients from nine unrelated families and their available family members were subjected to Sanger sequencing. Segregation analysis was performed for novel mutation. The effect of each mutation on protein stability and hydropathicity, as well as the pathogenicity prediction of all detected mutations were assessed using various in silico analysis tools.</div></div><div><h3>Results</h3><div>Six mutations including a novel and five previously reported mutations were identified in patients with different ethnicities. Three out of five known mutations were reported for the first time in Iran. Various common clinical manifestations and a rarely reported coexistence of celiac disease in biotinidase deficiency patients were observed. The novel missense variant c.787G &gt; A (p.Glu263Lys) was detected in exon 4 of the <em>BTD</em> gene, within the biotinidase-like domain of the BTD protein. This variation was found in two cousins of a family, both developed the same initial clinical presentation. In silico analyses revealed that this missense substitution decreased protein stability and increased protein hydrophilicity. Additionally, the known frameshift mutation c.1264delG (p.val422serfster59), was the most frequent allele in the studied population. We also predicted and visualized the effects of the novel and frameshift mutations on protein structure.</div></div><div><h3>Conclusion</h3><div>Our findings expanded the mutational spectrum of the <em>BTD</em> gene and provided valuable data on genotype-phenotype correlations, which helps in genetic counseling. Furthermore, the necessity of performing molecular analysis along with enzymatic analysis was highlighted by this study.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498274","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":"Comprehensive bioinformatics analysis of the prognostic value and immune infiltration of CAPN2 in pancreatic adenocarcinoma","authors":"Qiuyan Zhao ,&nbsp;Haoran Xie ,&nbsp;Xing Wang ,&nbsp;Jiabei Xie ,&nbsp;Jin Liu ,&nbsp;Yangqiu Bai ,&nbsp;Bowei Liu ,&nbsp;Hui Ding ,&nbsp;Shengli Kuang ,&nbsp;Bingyong Zhang","doi":"10.1016/j.gene.2024.149035","DOIUrl":"10.1016/j.gene.2024.149035","url":null,"abstract":"<div><h3>Background</h3><div>Pancreatic adenocarcinoma (PAAD) is a highly aggressive cancer with a poor prognosis, highlighting an urgent requirement for effective biomarkers for its early diagnosis and prognosis prediction. CAPN2, a calcium-dependent protease, has been implicated in various cancers, but its role in PAAD remains unclear.</div></div><div><h3>Methods</h3><div>In this study, we utilized multiple bioinformatics methods, including differential expression, survival, correlation, and enrichment analyses, to investigate the prognostic value of CAPN2 in PAAD using data from the TCGA and GEO databases. Additionally, the correlation between CAPN2 expression and the tumor microenvironment (TME), immunotherapy potential, and drug sensitivity was also explored.</div></div><div><h3>Results</h3><div>CAPN2 was upregulated in PAAD tissues and was correlated with higher tumor grade. And high expression of CAPN2 was significantly associated with reduced overall survival, establishing it as an independent prognostic biomarker for PAAD. Enrichment analysis implicated that CAPN2 was involved in multiple biological processes and pathways associated with tumor immunity. Furthermore, CAPN2 expression had a negative correlation with immune cell infiltration and a positive association with tumor mutational burden, which may have potential implications for immunotherapy strategies.</div></div><div><h3>Conclusions</h3><div>CAPN2 is a promising biomarker for PAAD prognosis and a potential therapeutic target. Its association with the TME and immunotherapy response highlights its importance in PAAD progression and patient outcomes, warranting further investigation into its role and potential clinical applications.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498270","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 assembly and characterization of the complete mitochondrial genome of Phellodendron amurense reveals three repeat‐mediated recombination","authors":"Junlin Liu ,&nbsp;Shaoshuai Yu ,&nbsp;Peng Lü ,&nbsp;Xun Gong ,&nbsp;Mengmeng Sun ,&nbsp;Min Tang","doi":"10.1016/j.gene.2024.149031","DOIUrl":"10.1016/j.gene.2024.149031","url":null,"abstract":"<div><div><em>Phellodendron amurense Rupr</em>., a rare herb renowned for its medicinal and ecological significance, has remained genetically unexplored at the mitochondrial level until now. This study presents the first-ever systematic assembly and annotation of the complete mitochondrial genome of <em>P. amurense</em>, achieved through a hybrid strategy combining Illumina and Nanopore sequencing data. The mitochondrial genome spans 566,285 bp with a GC content of 45.51 %, structured into two circular molecules. Our comprehensive analysis identified 32 protein-coding genes (PCGs), 33 tRNA genes, and 3 rRNA genes, alongside 181 simple sequence repeats, 19 tandem repeats, and 310 dispersed repeats. Notably, multiple genome conformations were predicted due to repeat-mediated homologous recombination. Additionally, we assembled the chloroplast genome, identifying 21 mitochondrial plastid sequences that provide insights into organelle genome interactions. A total of 380 RNA-editing sites within the mitochondrial PCGs were predicted, enhancing our understanding of gene regulation and function. Phylogenetic analysis using mitochondrial PCGs from 30 species revealed evolutionary relationships, confirming the homology between <em>P. amurense</em> and Citrus species. This foundational study offers a valuable genetic resource for the Rutaceae family, facilitating further research into genetic evolution and molecular diversity in plant mitochondrial genomes.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498272","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 identifies potential molecular mechanisms for growth of fast muscle in Chinese perch juvenile","authors":"Wei Zeng ,&nbsp;Yangyang Meng ,&nbsp;Junxin Ma ,&nbsp;Linxuan Zhang ,&nbsp;Wei Wang ,&nbsp;Yaxiong Pan ,&nbsp;Xin Zhu ,&nbsp;Wuying Chu","doi":"10.1016/j.gene.2024.149034","DOIUrl":"10.1016/j.gene.2024.149034","url":null,"abstract":"<div><div>Chinese perch (<em>Siniperca chuatsi</em>) is an important commercial fish species in China. Understanding the molecular mechanisms of growth and development of skeletal muscle is helpful for selection breeding and improving the growth rate of Chinese perch. We analyzed histological and transcriptomic differences in fast muscle of Chinese perch between 30 days post hatching (dph) and 60 dph using histological sections and high-throughput RNA-Seq. The results showed that the diameter of muscle fibers in 30 dph Chinese perch was mainly distributed in range of 30 − 40 μm, and that of 60 dph was primarily in the range of 40 − 50 μm. 34 differentially expressed genes (DEGs) were identified in the fast muscle of Chinese perch between 30 and 60 dph, of which 9 were up-regulated and 25 were down-regulated (60 dph vs 30 dph). The DEGs, including <em>MYH4</em>, <em>ENO3</em>, <em>Bag3, krt13 and krt18</em>, are associated with muscle cell differentiation and fusion in Chinese perch. The analysis of the protein–protein interaction network of DEGs revealed that <em>FOS</em>, <em>junb</em> and <em>EGR1</em> may involve in the development of fast muscle. KEGG enrichment results showed that the up-regulated genes in the 60 dph were associated with several pathways related to metabolism and protein synthesis, such as glycosphingolipid biosynthesis and aminoacyl-tRNA biosynthesis. The results suggest that the development of fast muscle in Chinese perch from 30 to 60 dph is accompanied by an increase in muscle fiber diameter and changes in gene expression related to muscle cell differentiation and protein synthesis.</div><div>Abbreviations: DEGs, differentially expressed genes; dph, days post hatching; FC, fold change; FDR, False Discovery Rate; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; MyHCs, Myosin heavy chains; qRT-PCR, quantitative real-time PCR.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498378","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":"Differentiation of long Non-Coding RNA expression profiles in three Fruiting stages of grape","authors":"Shahla Sahraei ,&nbsp;Nafiseh Mahdinezhad ,&nbsp;Abbasali Emamjomeh ,&nbsp;Kaveh Kavousi ,&nbsp;Mahmood Solouki ,&nbsp;Massimo Delledonne","doi":"10.1016/j.gene.2024.149029","DOIUrl":"10.1016/j.gene.2024.149029","url":null,"abstract":"<div><div>Grapes are considered a crucial fruit crop with extensive uses globally. Cluster compactness is an undesirable trait for the productivity of Yaghooti grape, and it reduces its desirability among consumers. The RNA-Seq data were analyzed in three stages of cluster development using the FEELnc software, leading to the identification of 849 lncRNAs. 183 lncRNAs were differentially expressed during cluster development stages. The GO and KEGG enrichment analyses of these lncRNAs revealed that they target 1,814 genes, including CKX, PG, PME, NPC2, and UGT. The analysis demonstrated a relationship between these lncRNAs and key processes such as grape growth and development, secondary metabolite synthesis, and resistance to both biotic and abiotic stresses. These findings, combined with molecular experiments on lncRNA interactions with other regulatory factors, could enhance Yaghooti grape quality and decrease cluster compactness.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498273","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":"The development of hooded awns in barley: From ectopic Kap1 expression to yield potential","authors":"Tian-jiang Liao ,&nbsp;Hui-yan Xiong ,&nbsp;Shun Sakuma ,&nbsp;Rui-jun Duan","doi":"10.1016/j.gene.2024.149036","DOIUrl":"10.1016/j.gene.2024.149036","url":null,"abstract":"<div><div>Awns in barley have different shapes including awnless, straight, hooded, crooked, and leafy awns. The hooded awns are characterized by an appendage of the lemma, which forms a trigonal or cap-shaped structure, and even blossoms and yields fruits on barley awn. In the lemma primordia of wild-type (straight awn), cells divide and elongate to form the straight awn. However, in the lemma primordia of <em>KNOX3</em> mutant (hooded awn), cells divide at various orientations without elongating, and they form hooded awns. This phenomenon is due to the upregulation of <em>KNOX3</em> expression via insertion of a tandem direct duplication of 305 bp in the intron IV. Here, we summarize the development of barley hooded awn research in the following two aspects: on the one hand, the morphology, development of hooded awns, and the expression regulation of the <em>KNOX3</em> gene. The latter includes ectopic expression of the <em>KNOX3</em> gene, gene interactions among awn-related genes, the regulatory relationship between class I KNOX genes and hormones, as well as the influence of abiotic stresses. On the other hand, the potential performance of hooded awns in barley for yield breeding is discussed. Hooded awns have potential application value in forage, which could compensate for the disadvantage of the long straight awn in the barley straw used for feed in modern cultivars. In addition, the hooded awn produces ectopic meristems to develop complete florets, which is an interesting question and helps to understand the development, adaptation, and evolution of plant floral organs.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498372","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":"IGFBP5 in osteosarcoma tumorigenesis: Gene expression profile among metastatic and non-metastatic patients","authors":"G.M. Guimarães ,&nbsp;F. Tesser-Gamba ,&nbsp;A.S. Petrilli ,&nbsp;M.T.S. Alves ,&nbsp;R.J. Garcia-Filho ,&nbsp;R. Oliveira ,&nbsp;S.R.C. Toledo","doi":"10.1016/j.gene.2024.149026","DOIUrl":"10.1016/j.gene.2024.149026","url":null,"abstract":"<div><div>Osteosarcoma (OS) is the most frequent primary malignant bone tumor among children and adolescents, with a peak of incidence in the second decade of life. The presence of metastasis at diagnosis in OS patients significantly decreases the chances of survival and new therapy approaches are needed. The <em>IGFBP5</em> gene is related to osteoblasts metabolism and some studies have pointed out a role of its low expressions in OS development and metastasis. In this study, we aimed to establish an <em>IGFBP5</em> gene expression profile among metastatic and non-metastatic OS patients throughout the treatment and development of the disease. Fresh-frozen tumor samples were obtained from 40 patients admitted to treatment at the Pediatric Oncology Institute (IOP/GRAACC/UNIFESP) and divided by clinical status: metastatic or non-metastatic disease. For each patient, samples before and after chemotherapy treatment were obtained, as well as metastasis and lung tissue surrounding metastasis samples from the metastatic patients. A quantitative real-time PCR was used to investigate <em>IGFBP5</em> expression. Our analyses demonstrate that non-metastatic patients presented lower <em>IGFBP5</em> expression in their pre-chemotherapy samples compared with metastatic patients, suggesting that low expressions of this gene could help triggering the OS tumorigenesis but that its action alone is not sufficient to activate the metastatic process. Heterogeneity in <em>IGFBP5</em> expressions within groups was also seen. We observed that <em>IGFBP5</em> and two MAPK genes, a downstream pathway in the <em>IGFBP5</em> axis, are differentially expressed in OS samples of non-metastatic patients. Further investigation about these genes’ modulations might lead to a better understanding of metastasis development in OS.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498376","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}