Genes & genomics最新文献

{"title":"Optimizing Bangkaew dog breed identification using DNA technology","authors":"Chananya Patta, Worapong Singchat, Chadaphon Thatukan, Wattanawan Jaito, Nichakorn Kumnan, Piangjai Chalermwong, Thitipong Panthum, Trifan Budi, Wongsathit Wongloet, Pish Wattanadilokchatkun, Thanyapat Thong, Syed Farhan Ahmad, Narongrit Muangmai, Kyudong Han, Prateep Duengkae, Rattanin Phatcharakullawarawat, Kornsorn Srikulnath","doi":"10.1007/s13258-024-01510-0","DOIUrl":"https://doi.org/10.1007/s13258-024-01510-0","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Background</h3><p>The Bangkaew dog is an indigenous dog breed in the Phitsanulok province of Thailand. This breed is recognized by the Fédération Cynologique Internationale (FCI), a global canine organization. The unique traits of the Bangkaew breed lead to purebred selection for breeding, while only their traits and pedigree from parental history are recorded. Determination of the risk of inbreeding depression and the origin of unknown DNA profiles is essential due to the challenges in predicting puppy characteristics, which are crucial for breed management and conservation.</p><h3 data-test=\"abstract-sub-heading\">Objective</h3><p>This study aimed to emphasize that current allelic frequency data for the Bangkaew dog breed must be considered for precise individual identification.</p><h3 data-test=\"abstract-sub-heading\">Methods</h3><p>Approximately 82 Bangkaew dogs from various Thai localities were studied using 15 microsatellite markers for genotypic monitoring and individual identification. Maternal genetic inheritance was assessed via mtDNA D-loop analysis.</p><h3 data-test=\"abstract-sub-heading\">Results</h3><p>The results revealed high genetic diversity in the Bangkaew breed, indicating low potential for inbreeding. We also found that using a 15 loci microsatellite panel was effective for the identification of Bangkaew dogs. The optimized 10 loci microsatellite genotyping panel developed in this study presents improved identification testing efficiency, promoting both time- and cost-effectiveness.</p><h3 data-test=\"abstract-sub-heading\">Conclusion</h3><p>Analysis of microsatellite DNA markers in Bangkaew dogs using an optimized panel of 10 loci selected from 15 loci effectively facilitated individual identification. This approach not only enhances time and cost efficiency, but also provides accurate allelic frequency estimates, which are crucial for the realistic evaluation of DNA evidence.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140838625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The transcriptome response of Enterobacter sp. S-33 is modulated by low pH-stress","authors":"Kiran Kumari, Parva Kumar Sharma, Rajnish Prakash Singh","doi":"10.1007/s13258-024-01513-x","DOIUrl":"https://doi.org/10.1007/s13258-024-01513-x","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Background</h3><p>Acidic environments naturally occur worldwide and uncontrolled use of agricultural practices may also cause acidification of soils. The development of acidic conditions disturbs the establishment of efficient microbial populations in their natural niches. The survival of <i>Enterobacter</i> species under acidic stress remains poorly understood.</p><h3 data-test=\"abstract-sub-heading\">Objective</h3><p>This study aimed to investigate the survival of an environmental isolate <i>Enterobacter</i> sp. S-33 under acidic stress and to identify the various genes involved in stress protection at the global gene transcription level. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to environmental pH changes.</p><h3 data-test=\"abstract-sub-heading\">Methods</h3><p>We used the next-generation sequencing (NGS) method to analyze the expression (up-regulation &amp; down-regulation) of genes under varying pH conditions.</p><h3 data-test=\"abstract-sub-heading\">Results</h3><p>A total of 4214 genes were differentially expressed under acidic conditions (pH 5.0), with 294 up-regulated and 167 down-regulated. At pH 6.0, 50 genes were significantly expressed, of which 34 and 16 were identified as up-regulated and down-regulated, respectively. Many of the up-regulated genes were involved in carbohydrate metabolism, amino acid transport &amp; metabolism, and the most down-regulated genes were related to post-translational modification, lipid transport &amp; metabolism, etc. The observed transcriptomic regulation of genes and pathways identified that <i>Enterobacter</i> reduced its post-translational modification, lipid transport &amp; metabolism, and increased carbohydrate metabolism, amino acid metabolism &amp; transport, energy production &amp; conversion to adapt and grow in acidic stress.</p><h3 data-test=\"abstract-sub-heading\">Conclusions</h3><p>The present work provides in-depth information on the characterization of genes associated with tolerance or adaptation to acidic stress of <i>Enterobacter</i> bacterium.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140838167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery and genome-wide characterization of a novel miniature inverted repeat transposable element reveal genome-specific distribution in Glycine","authors":"Hümeyra Yıldız Akkamış, Emir Can Kaya, Ahmet L. Tek","doi":"10.1007/s13258-024-01519-5","DOIUrl":"https://doi.org/10.1007/s13258-024-01519-5","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Background</h3><p>Miniature inverted repeat transposable elements (MITEs) are a dynamic component responsible for genome evolution. Tourist MITEs are derived from and mobilized by elements from the harbinger superfamily.</p><h3 data-test=\"abstract-sub-heading\">Objective</h3><p>In this study, a novel family of Tourist-like MITE was characterized in wild soybean species <i>Glycine falcata</i>. The new GftoMITE1 was initially discovered as an insertional polymorphism of the centromere-specific histone H3 (CenH3) gene in <i>G. falcata</i>.</p><h3 data-test=\"abstract-sub-heading\">Methods</h3><p>Using polymerase chain reaction, cloning and sequencing approaches, we showed a high number of copies of the GftoMITE1 family. Extensive bioinformatic analyses revealed the genome-level distribution and locus-specific mapping of GftoMITE1 members in Glycine species.</p><h3 data-test=\"abstract-sub-heading\">Results</h3><p>Our results provide the first extensive characterization of the GftoMITE1 family and contribute to the understanding of the evolution of MITEs in the Glycine genus. Genome-specific GftoMITE1 was prominent in perennial wild soybean species, but not in annual cultivated soybean (<i>Glycine max</i>) or its progenitor (<i>Glycine soja</i>).</p><h3 data-test=\"abstract-sub-heading\">Conclusions</h3><p>We discuss that the GftoMITE1 family reveals a single rapid amplification in <i>G. falcata</i> and could have potential implications for gene regulation and soybean breeding as an efficient genetic marker for germplasm utilization in the future.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140812457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Helicobacter pylori infection induces gastric cancer cell malignancy by targeting HOXA-AS2/miR-509-3p/MMD2 axis","authors":"Si Cheng, Yu Jia, Juan Wu, Jiguang Li, Yan Cao","doi":"10.1007/s13258-024-01500-2","DOIUrl":"https://doi.org/10.1007/s13258-024-01500-2","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Background</h3><p><i>Helicobacter pylori</i> (Hp) infection is considered to be the strongest risk factor for gastric cancer (GC). Long non-coding RNA HOXA cluster antisense RNA 2 (HOXA-AS2) has been indicated to be significantly related to Hp infection in GC patients.</p><h3 data-test=\"abstract-sub-heading\">Objective</h3><p>To investigate the detailed role and molecular mechanism of lncRNA HOXA-AS2 in Hp-induced GC.</p><h3 data-test=\"abstract-sub-heading\">Methods</h3><p>GC cells were treated with Hp filtrate for cell infection. Bioinformatics tools were utilized for survival analysis and prediction of HOXA-AS2 downstream molecules. Western blotting and RT-qPCR were utilized for assessing protein and RNA levels, respectively. Flow cytometry, colony formation and CCK-8 assays were implemented for testing HOXA-AS2 functions in Hp-infected GC cells. HOXA-AS2 localization in cells was determined by subcellular fractionation assay. The relationship between RNAs were measured by luciferase reporter assay.</p><h3 data-test=\"abstract-sub-heading\">Results</h3><p>Hp infection induced HOXA-AS2 upregulation in GC cells. Knocking down HOXA-AS2 restrained cell proliferation but promoted cell apoptosis with Hp infection. HOXA-AS2 bound to miR-509-3p, and miR-509-3p targeted monocyte to macrophage differentiation associated 2 (MMD2). Overexpressing MMD2 reversed HOXA-AS2 depletion-mediated suppression on cell aggressiveness with Hp infection.</p><h3 data-test=\"abstract-sub-heading\">Conclusion</h3><p>Hp infection induces the aggressiveness of GC cells by regulating HOXA-AS2/miR-509-3p/MMD2 axis.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140566193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular characterization and expression pattern of Rubisco activase gene GhRCAβ2 in upland cotton (Gossypium hirsutum L.).","authors":"Maoni Chao, Ling Huang, Jie Dong, Yu Chen, Genhai Hu, Qiufang Zhang, Jinbao Zhang, Qinglian Wang","doi":"10.1007/s13258-024-01494-x","DOIUrl":"10.1007/s13258-024-01494-x","url":null,"abstract":"<p><strong>Background: </strong>Rubisco activase (RCA) is a pivotal enzyme that can catalyse the activation of Rubisco in carbon assimilation pathway. Many studies have shown that RCA may be a potential target for genetic manipulation aimed at enhancing photosynthetic efficiency and crop yield.</p><p><strong>Objective: </strong>To understand the biological function of the GhRCAβ2 gene in upland cotton, we cloned the coding sequence (CDS) of the GhRCAβ2 gene and investigated its sequence features, evolutionary relationship, subcellular localization, promoter sequence and expression pattern.</p><p><strong>Methods: </strong>The bioinformatics tools were used to analyze the sequence features of GhRCAβ2 protein. Transient transformation of Arabidopsis mesophyll protoplasts was performed to determine the subcellular localization of the GhRCAβ2 protein. The expression pattern of the GhRCAβ2 gene was examined by analyzing transcriptome data and using the quantitative real-time PCR (qRT-PCR).</p><p><strong>Results: </strong>The full-length CDS of GhRCAβ2 was 1317 bp, and it encoded a protein with a chloroplast transit peptide. The GhRCAβ2 had two conserved ATP-binding domains, and did not have the C-terminal extension (CTE) domain that was unique to the RCA α-isoform in plants. Evolutionarily, GhRCAβ2 was clustered in Group A, and had a close evolutionary relationship with the soybean RCA. Western blot analysis demonstrated that GhRCAβ2 was immunoreactive to the RCA antibody displaying a molecular weight similar to that of the RCA β-isoform. The GhRCAβ2 protein was found in chloroplast, aligning with its role as a vital enzyme in the process of photosynthesis. The GhRCAβ2 gene had a leaf tissue-specific expression pattern, and the yellow-green leaf mutant exhibited a decreased expression of GhRCAβ2 in comparison to the wild-type cotton plants. The GhRCAβ2 promoter contained several cis-acting elements that respond to light, phytohormones and stress, suggesting that the expression of GhRCAβ2 may be regulated by these factors. An additional examination of stress response indicated that GhRCAβ2 expression was influenced by cold, heat, salt, and drought stress. Notably, diverse expression pattern was observed across different stress conditions. Additionally, low phosphorus and low potassium stress may result in a notable reduction in the expression of GhRCAβ2 gene.</p><p><strong>Conclusion: </strong>Our findings will establish a basis for further understanding the function of the GhRCAβ2 gene, as well as providing valuable genetic knowledge to improve cotton photosynthetic efficiency and yield under challenging environmental circumstances.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139697260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Human umbilical cord mesenchymal stem cells overexpressing RUNX1 promote tendon-bone healing by inhibiting osteolysis, enhancing osteogenesis and promoting angiogenesis.","authors":"Dan Guo, Jian Yang, Dianwei Liu, Pei Zhang, Hao Sun, Jingcheng Wang","doi":"10.1007/s13258-023-01478-3","DOIUrl":"10.1007/s13258-023-01478-3","url":null,"abstract":"<p><strong>Background: </strong>Rotator cuff injury (RCI) is a common shoulder injury, which is difficult to be completely repaired by surgery. Hence, new strategies are needed to promote the healing of tendon-bone.</p><p><strong>Objective: </strong>We aimed to investigate the effect of human umbilical cord mesenchymal stem cells (hUC-MSCs) overexpressing RUNX1 on the tendon-bone healing after RCI, and to further explore its mechanism.</p><p><strong>Methods: </strong>Lentiviral vector was used to mediate the overexpression of RUNX1. RUNX1-overexpressed UCB-MSCs (referred to as MSC-RUNX1) were co-cultured with osteoclasts, and TRAP staining was performed to observe the formation of osteoclasts. Then MSC-RUNX1 was cultured in osteogenic differentiation medium, Alizarin red staining was conducted to detect osteogenic differentiation. The expression of markers of osteogenesis and osteoclast was detected by RT-qPCR. EA. hy926 cells were co-cultured with MSC-RUNX1. Transwell assay was used to detect the migration, and the expression of angiogenesis related-genes VEGF and TGF-β was detected by RT-qPCR. The rat rotator cuff reconstruction model was established and MSCs were injected at the tendon-bone junction. Biomechanical test and micro-CT scanning were performed, and HE, Masson and Alcian Blue staining were used for histological evaluation of tendon-bone healing. TUNEL and PCNA immunofluorescence (IF) staining were performed to evaluate apoptosis and proliferation at the tendon-bone healing site. The levels of TNF-α, IL-6 and IL-8 in serum were detected by ELISA. The expression of CD31 and Endomucin that related to angiogenesis was detected by IF. Safranin O-fast and TRAP/CD40L immunohistochemical staining were used to assess the levels of osteoclasts and osteoblasts at the tendon-bone healing site.</p><p><strong>Results: </strong>hUC-MSCs overexpressing RUNX1 inhibited osteoclast formation and promoted osteogenic differentiation. MSC-RUNX1 could promote the migration and tube formation of EA. hy926 cells, and up-regulate the levels of VEGF and TGF-β. Model mice treated with MSC-RUNX1 partially restored the biomechanical indexes. Treatment of MSC-RUNX1 obviously increased the bone density, accompanied by the formation of new bone. In vivo experiments showed that MSC-RUNX1 treatment could promote tendon-bone healing and inhibit inflammatory response in rats. MSC-RUNX1 treatment also promoted angiogenesis at the tendon-bone healing site, while inhibiting osteoclast formation and promoting osteogenic differentiation.</p><p><strong>Conclusion: </strong>hUC-MSCs overexpressing RUNX1 can inhibit the formation of osteoclasts and differentiation of osteoblasts, promote angiogenesis and inhibit inflammation, thereby promoting tendon-bone healing after RCI.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139097722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical report and genetic analysis of a novel variant in ZMIZ1 causing neurodevelopmental disorder with dysmorphic factors and distal skeletal anomalies in a Chinese family.","authors":"Liting He, Yao Wang, Jiahua Pan, Limin Guo, Haoquan Zhou, Lan Zhang","doi":"10.1007/s13258-023-01480-9","DOIUrl":"10.1007/s13258-023-01480-9","url":null,"abstract":"<p><strong>Background: </strong>Neurodevelopmental disorder with dysmorphic factors and distal skeletal anomalies (NEDDFSA) is a rare and phenotypically variable disorder. The zinc finger MIZ-type containing 1 gene (ZMIZ1) is a causative gene of NEDDFSA that encodes a protein inhibitor of the activated STAT-like family transcriptional regulator. Given the rarity of reported NEDDFSA cases, new phenotypes and genotypes of this disorder are still being discovered.</p><p><strong>Objective: </strong>This study describes the phenotype characteristics of a Chinese NEDDFSA family caused by a novel ZMIZ1 variant.</p><p><strong>Methods: </strong>We reviewed the clinical phenotype of a Chinese patient with NEDDFSA and performed whole-exome sequencing (WES) of the patient's family. We simulated the potential biological harmfulness of the mutant protein. Plasmids were constructed and used for western blot and immunofluorescence assays to analyze protein expression levels.</p><p><strong>Results: </strong>The patient was a 6-month-old male infant who exhibited dysmorphic facial features, neurodevelopmental abnormalities, congenital heart disease, and previously unreported genitourinary system anomalies. WES revealed a non-frameshift deletion variant in ZMIZ1 (NM_020338.4: c.858_875del, p.Val288_Ala293del), resulting in a structural alteration in the protein's alanine-rich domain. Western blot and immunofluorescence assays indicated a significant decrease in the expression level of the mutant ZMIZ1 protein compared to the wild-type protein.</p><p><strong>Conclusion: </strong>The clinical manifestations of this patient may be associated with the ZMIZ1 variant, and the structural alteration in the alanine-rich domain of the ZMIZ1 protein may contribute to a more complex disease phenotype. These results expand the genotype-phenotype correlation of ZMIZ1.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138800820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expression of ethylene biosynthetic genes during flower senescence and in response to ethephon and silver nitrate treatments in Osmanthus fragrans.","authors":"Hui Qiu, Yiwen Chen, Jianxin Fu, Chao Zhang","doi":"10.1007/s13258-023-01489-0","DOIUrl":"10.1007/s13258-023-01489-0","url":null,"abstract":"<p><strong>Background: </strong>Sweet osmanthus (Osmanthus fragrans) is an ornamental evergreen tree species in China, whose flowers are sensitive to ethylene. The synthesis of ethylene is controlled by key enzymes and restriction enzymes, 1-aminocyclopropane-1-carboxylic acid synthase (ACS) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), which are encoded by multigene families. However, the key synthase responsible for ethylene regulation in O. fragrans is still unknown.</p><p><strong>Objective: </strong>This study aims to screen the key ethylene synthase genes of sweet osmanthus flowers in response to ethylene regulation.</p><p><strong>Methods: </strong>In this study, we used the ACO and ACS sequences of Arabidopsis thaliana to search for homologous genes in the O. fragrans petal transcriptome database. These genes were also analyzed bioinformatically. Finally, the expression levels of O. fragrans were compared before and after senescence, as well as after ethephon and silver nitrate treatments.</p><p><strong>Results: </strong>The results showed that there are five ACO genes and one ACS gene in O. fragrans transcriptome database, and the phylogenetic tree revealed that the proteins encoded by these genes had high homology to the ACS and ACO proteins in plants. Sequence alignment shows that the OfACO1-5 proteins have the 2OG-Fe(II) oxygenase domain, while OfACS1 contains seven conserved domains, as well as conserved amino acids in transaminases and glutamate residues related to substrate specificity. Expression analysis revealed that the expression levels of OfACS1 and OfACO1-5 were significantly higher at the early senescence stage compared to the full flowering stage. The transcripts of the OfACS1, OfACO2, and OfACO5 genes were upregulated by treatment with ethephon. However, out of these three genes, only OfACO2 was significantly downregulated by treatment with AgNO₃.</p><p><strong>Conclusion: </strong>Our study found that OfACO2 is an important synthase gene in response to ethylene regulation in sweet osmanthus, which would provide valuable data for further investigation into the mechanisms of ethylene-induced senescence in sweet osmanthus flowers.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioinformatics analysis and experimental validation reveal that CDC20 overexpression promotes bladder cancer progression and potential underlying mechanisms.","authors":"Yuan Liu, Shao-Hui Zou, Xin Gao","doi":"10.1007/s13258-024-01505-x","DOIUrl":"10.1007/s13258-024-01505-x","url":null,"abstract":"<p><strong>Background: </strong>Bladder cancer is a prevalent malignancy. CDC20, a pivotal cell cycle regulator gene, plays a significant role in tumour cell proliferation, but its role in bladder cancer remains unclear.</p><p><strong>Objective: </strong>This study aimed to analyse CDC20 expression in bladder cancer and explore its roles in tumour progression, treatment response, patient prognosis, and cellular proliferation mechanisms.</p><p><strong>Methods: </strong>We systematically analysed CDC20 expression in bladder cancer using bioinformatics. Our study investigated the impact of CDC20 on chemotherapy and radiotherapy sensitivity, patient prognosis, and changes in CDC20 methylation levels. We also explored the role and potential underlying mechanisms of CDC20 in bladder cancer cell growth. We used lentiviral transfection to downregulate CDC20 expression in 5637 and T24 cells, followed by CCK-8, colony formation, scratch, invasion, apoptosis, and cell cycle analyses.</p><p><strong>Results: </strong>CDC20 is highly expressed in bladder cancer and is significantly correlated with poor prognosis. Moreover, CDC20 demonstrated high diagnostic potential for bladder cancer (AUC > 0.9). The tumour methylation levels of CDC20 in tumour tissues markedly decreased compared with those in normal tissues, and lower methylation levels were associated with a worse prognosis. Elevated CDC20 expression is linked to increased mutation burden. Our findings suggested a potential association between high CDC20 expression and resistance to chemotherapy and radiotherapy, as CDC20 expression may impact immune cell infiltration levels. Mechanistic analysis revealed the influence of CDC20 on bladder cancer cell proliferation through cell cycle-related pathways. According to the cell experiments, CDC20 downregulation significantly impedes bladder cancer cell proliferation and invasion, leading to G1 phase arrest.</p><p><strong>Conclusion: </strong>Aberrantly high CDC20 expression promotes tumour progression in bladder cancer, resulting in a poor prognosis, and may also constitute a promising therapeutic target.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140027874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Childhood-related neural genotype-phenotype in ATP1A3 mutations: comprehensive analysis.","authors":"Osama Y Muthaffar, Asma Alqarni, Jumana A Shafei, Sarah Y Bahowarth, Anas S Alyazidi, Muhammad Imran Naseer","doi":"10.1007/s13258-023-01481-8","DOIUrl":"10.1007/s13258-023-01481-8","url":null,"abstract":"<p><strong>Background: </strong>ATP1A3 is a gene that encodes the ATPase Na + /K + transporting subunit alpha-3 isoenzyme that is widely expressed in GABAergic neurons. It maintains metabolic balance and neurotransmitter movement. These pathways are essential for the proper functioning of the nervous system. A mutation in the ATP1A3 gene demonstrates remarkable genotype-phenotype heterogeneity.</p><p><strong>Objectives: </strong>To provide insight into patients with ATP1A3 mutation.</p><p><strong>Material and methods: </strong>These cases were identified using next generation sequencing. The patients' clinical and genetic data were retrieved. Detailed revision of the literature was conducted to illustrate and compare findings. The clinical, genetical, neuroimaging, and electrophysiological data of all pediatric patients were extracted.</p><p><strong>Results: </strong>The study included 14 females and 12 males in addition to two novel females cases. Their mean current age is 6.3 ± 4.24 years. There were 11.54% preterm pregnancies with 5 cases reporting pregnancy complications. Mean age of seizure onset was 1.07 ± 1.06 years. Seizure semiology included generalized tonic-clonic, staring spells, tonic-clonic, and others. Levetiracetam was the most frequently used Anti-seizure medication. The three most frequently reported classical symptoms included alternating hemiplegia of childhood (50%), cerebellar ataxia (50%), and optic atrophy (23.08%). Non-classical symptoms included dystonia (73.08%), paroxysmal dyskinesias (34.62%), and encephalopathy (26.92%). Developmental delay was reported among 84.62% in cognitive, 92.31% in sensorimotor, 80.77% in speech, and 76.92% in socioemotional. EEG and MRI were non-specific.</p><p><strong>Conclusion: </strong>Our study demonstrated high heterogeneity among patients with pathogenic variants in the ATP1A3 gene. Such variation is multifactorial and can be a predisposition of wide genetic and clinical variables. Many patients shared few similarities in their genetic map including repeatedly reported de novo, heterozygous, mutations in the gene. Clinically, higher females prevalence of atypical presentation was noted. These findings are validated with prior evidence and the comprehensive analysis in this study.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139502338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}