Functional & Integrative Genomics最新文献_第3页

Hybrid-genome sequence analysis of Enterobacter cloacae FACU and morphological characterization: insights into a highly arsenic-resistant strain 衣腔肠杆菌 FACU 的杂交基因组序列分析和形态特征：对高砷抗性菌株的认识。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-25 DOI: 10.1007/s10142-024-01441-9

Abdelhadi A. Abdelhadi, Nagwa I. Elarabi, Saifeldeen M. Ibrahim, Mostafa A. Abdel-Maksoud, Heba A. R. Abdelhaleem, Saeedah Almutairi, Abdul Malik, Bushra Hafeez Kiani, Ahmed R. Henawy, Asmaa A. Halema

{"title":"Hybrid-genome sequence analysis of Enterobacter cloacae FACU and morphological characterization: insights into a highly arsenic-resistant strain","authors":"Abdelhadi A. Abdelhadi, Nagwa I. Elarabi, Saifeldeen M. Ibrahim, Mostafa A. Abdel-Maksoud, Heba A. R. Abdelhaleem, Saeedah Almutairi, Abdul Malik, Bushra Hafeez Kiani, Ahmed R. Henawy, Asmaa A. Halema","doi":"10.1007/s10142-024-01441-9","DOIUrl":"10.1007/s10142-024-01441-9","url":null,"abstract":"<div><p>Many organisms have adapted to survive in environments with high levels of arsenic (As), a naturally occurring metalloid with various oxidation states and a common element in human activities. These organisms employ diverse mechanisms to resist the harmful effects of arsenic compounds. Ten arsenic-resistant bacteria were isolated from contaminated wastewater in this study. The most efficient bacterial isolate able to resist 15,000 ppm Na<sub>2</sub>HAsO<sub>4</sub>·7H<sub>2</sub>O was identified using the <i>16S rRNA</i> gene and whole genome analysis as <i>Enterobacter cloacae</i> FACU. The arsenic <i>E. cloacae</i> FACU biosorption capability was analyzed. To further unravel the genetic determinants of As stress resistance, the whole genome sequence of <i>E. cloacae</i> FACU was performed. The FACU complete genome sequence consists of one chromosome (5.7 Mb) and two plasmids, pENCL 1 and pENCL 2 (755,058 and 1155666 bp, respectively). 7152 CDSs were identified in the <i>E. cloacae</i> FACU genome. The genome consists of 130 genes for tRNA and 21 for rRNAs. The average G + C content was found to be 54%. Sequencing analysis annotated 58 genes related to resistance to many heavy metals, including 16 genes involved in arsenic efflux transporter and arsenic reduction (five <i>arsRDABC</i> genes) and 42 genes related to lead, zinc, mercury, nickel, silver, copper, cadmium and chromium in FACU. Scanning electron microscopy (SEM) confirmed the difference between the morphological responses of the As-treated FACU compared to the control strain. The study highlights the genes involved in the mechanism of As stress resistance, metabolic pathways, and potential activity of <i>E. cloacae</i> FACU at the genetic level.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338899","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}

引用次数: 0

m6A methylation in myocardial tissue of septic mice analyzed using MeRIP/m6A-sequencing and RNA-sequencing 使用 MeRIP/m6A 测序和 RNA 测序分析脓毒症小鼠心肌组织中的 m6A 甲基化。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-25 DOI: 10.1007/s10142-024-01452-6

Xue Liang, Xiaotong Hu, Jiao Li, Boyang Zhang, Tianshu Gu, Hualing Wang, Mingzhong Zhang, Xiaodong Xia, Siyu Guan, Wenfeng Shangguan, Shuai Miao, Weiding Wang, Hao Zhang, Zhiqiang Zhao, Lijun Wang

{"title":"m6A methylation in myocardial tissue of septic mice analyzed using MeRIP/m6A-sequencing and RNA-sequencing","authors":"Xue Liang, Xiaotong Hu, Jiao Li, Boyang Zhang, Tianshu Gu, Hualing Wang, Mingzhong Zhang, Xiaodong Xia, Siyu Guan, Wenfeng Shangguan, Shuai Miao, Weiding Wang, Hao Zhang, Zhiqiang Zhao, Lijun Wang","doi":"10.1007/s10142-024-01452-6","DOIUrl":"10.1007/s10142-024-01452-6","url":null,"abstract":"<div><p>Septic cardiomyopathy is a secondary myocardial injury caused by sepsis. N6-methyl-adenosine (m6A) modification is involved in the pathological progression of septic cardiomyopathy; however, the pathological mechanism remains unclear. In this study, we identified the overall m6A modification pattern in septic myocardial injury and determined its potential interactions with differentially expressed genes (DEGs). A sepsis mouse model exhibiting septic symptoms and myocardial tissue damage was induced by lipopolysaccharide (LPS). LPS-induced septic myocardial tissues and control myocardial tissues were subjected to methylated RNA immunoprecipitation sequencing and RNA sequencing to screen for differentially expressed m6A peaks and DEGs. We identified 859 significantly m6A-modified genes in septic myocardial tissues, including 432 upregulated and 427 downregulated genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to explore the biological importance of differentially expressed m6A methylated genes and DEGs. Differentially expressed m6A methylated genes were enriched in immune- and inflammation-related pathways. Conjoint analysis revealed co-expression of differentially expressed m6A genes and DEGs, including genes that were upregulated or downregulated and those showing opposite trends. High expression of m6A-related genes (<i>WTAP</i> and <i>IGF2BP2</i>), interleukin-17, and interleukin-17 pathway-related genes (<i>MAPK11</i> and <i>TRAF3IP2</i>) was verified using reverse transcription-quantitative PCR. We confirmed the presence of m6A modification of the transcriptome and m6A-mediated gene expression in septic myocardial tissues.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338901","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}

引用次数: 0

Molecular analyses of the tubby-like protein gene family and their response to salt and high temperature in the foxtail millet (Setaria italica) 狐尾黍（Setaria italica）类管蛋白基因家族及其对盐和高温反应的分子分析。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-25 DOI: 10.1007/s10142-024-01458-0

Zhuanzhuan Jiang, Xiaoqi Chen, Lingling Ruan, Yan Xu, Ke Li

{"title":"Molecular analyses of the tubby-like protein gene family and their response to salt and high temperature in the foxtail millet (Setaria italica)","authors":"Zhuanzhuan Jiang, Xiaoqi Chen, Lingling Ruan, Yan Xu, Ke Li","doi":"10.1007/s10142-024-01458-0","DOIUrl":"10.1007/s10142-024-01458-0","url":null,"abstract":"<div><p>Tubby-like proteins (TLPs) are a group of proteins found in both eukaryotes and prokaryotes. They are significant in various physiological and biochemical processes, especially in plants’ response to abiotic stress. However, the role of TLP in foxtail millet (<i>Setaria italica</i>) remains unclear. The millet genome has 16 members of the TLP family with typical Tub domains, which can be sorted into five subgroups based on gene structure, motif, and protein domain distribution. <i>SiTLPs</i> were discovered to be predominantly located in the nucleus and also had extracellular distribution. The interspecific evolutionary analysis indicated that <i>SiTLPs</i> had a closer evolutionary relationship with monocots and were consistent with the morphological classification of foxtail millet. When subjected to salt stress, the abundance of <i>SiTLP</i> was affected, and qRT-PCR results showed that the expression levels of certain <i>SiTLP</i> members were induced by salt stress while others remained unresponsive. Except for <i>SiTLP14</i>, all other <i>SiTLP</i> genes were up-regulated in response to high-temperature stress, implying a potentially crucial role for <i>SiTLP</i> in mitigating high-temperature-induced damage. This study provides valuable insights into understanding the functional significance of the <i>TLP</i> gene family in foxtail millet.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338902","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}

引用次数: 0

Programmed cell death and melatonin: A comprehensive review 程序性细胞死亡与褪黑激素：全面综述。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-24 DOI: 10.1007/s10142-024-01454-4

Mahdi Rafiyian, Russel J. Reiter, Sayyed Mehdi Rasooli Manesh, Reza Asemi, Mehran Sharifi, Sotoudeh Mohammadi, Mohammad Ali Mansournia, Zatollah Asemi

引用次数: 0

Ischemic cardiac stromal fibroblast-derived protein mediators in the infarcted myocardium and transcriptomic profiling at single cell resolution 缺血性心肌基质成纤维细胞衍生蛋白介质在梗死心肌中的作用以及单细胞分辨率的转录组分析。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-20 DOI: 10.1007/s10142-024-01457-1

Ed Cha, Sung Ho Hong, Taj Rai, Vy La, Pranav Madabhushi, Darren Teramoto, Cameron Fung, Pauline Cheng, Yu Chen, Angelo Keklikian, Jeffrey Liu, William Fang, Finosh G. Thankam

{"title":"Ischemic cardiac stromal fibroblast-derived protein mediators in the infarcted myocardium and transcriptomic profiling at single cell resolution","authors":"Ed Cha, Sung Ho Hong, Taj Rai, Vy La, Pranav Madabhushi, Darren Teramoto, Cameron Fung, Pauline Cheng, Yu Chen, Angelo Keklikian, Jeffrey Liu, William Fang, Finosh G. Thankam","doi":"10.1007/s10142-024-01457-1","DOIUrl":"10.1007/s10142-024-01457-1","url":null,"abstract":"<div><p>This article focuses on screening the major secreted proteins by the ischemia-challenged cardiac stromal fibroblasts (CF), the assessment of their expression status and functional role in the post-ischemic left ventricle (LV) and in the ischemia-challenged CF culture and to phenotype CF at single cell resolution based on the positivity of the identified mediators. The expression level of CRSP2, HSP27, IL-8, Cofilin-1, and HSP90 in the LV tissues following coronary artery bypass graft (CABG) and myocardial infarction (MI) and CF cells followed the screening profile derived from the MS/MS findings. The histology data unveiled ECM disorganization, inflammation and fibrosis reflecting the ischemic pathology. CRSP2, HSP27, and HSP90 were significantly upregulated in the LV-CABG tissues with a concomitant reduction ion LV-MI whereas Cofilin-1, IL8, Nrf2, and Troponin I were downregulated in LV-CABG and increased in LV-MI. Similar trends were exhibited by ischemic CF. Single cell transcriptomics revealed multiple sub-phenotypes of CF based on their respective upregulation of CRSP2, HSP27, IL-8, Cofilin-1, HSP90, Troponin I and Nrf2 unveiling pathological and pro-healing phenotypes. Further investigations regarding the underlying signaling mechanisms and validation of sub-populations would offer novel translational avenues for the management of cardiac diseases.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11415418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142278564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

lncRNA HOTAIR and Cardiovascular diseases lncRNA HOTAIR 与心血管疾病

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-19 DOI: 10.1007/s10142-024-01444-6

Sina Taghvimi, Elahe Soltani Fard, Seyyed Hossein Khatami, Sara Zafaranchi Z. M., Mortaza Taheri-Anganeh, Ahmad Movahedpour, Hassan Ghasemi

{"title":"lncRNA HOTAIR and Cardiovascular diseases","authors":"Sina Taghvimi, Elahe Soltani Fard, Seyyed Hossein Khatami, Sara Zafaranchi Z. M., Mortaza Taheri-Anganeh, Ahmad Movahedpour, Hassan Ghasemi","doi":"10.1007/s10142-024-01444-6","DOIUrl":"10.1007/s10142-024-01444-6","url":null,"abstract":"<div><p>Cardiovascular diseases (CVDs) a major contributor to global mortality rates, with a steadily rising prevalence observed across the world. Understanding the molecular mechanisms that underlie the signaling pathways implicated in the pathogenesis of CVDs represents a salient and advantageous avenue toward the development of precision and targeted therapeutics. A recent development in CVDs research is the discovery of long non-coding RNAs (lncRNAs), which are now understood to have crucial roles in the onset and development of several pathophysiological processes. The distinct expression patterns exhibited by lncRNAs in various CVDs contexts, present a significant opportunity for their utilization as both biomarkers and targets for therapeutic intervention. Among the various identified lncRNAs, HOX antisense intergenic RNA (HOTAIR) functions as signaling molecules that are significantly implicated in the pathogenesis of cardiovascular disorders in response to risk factors. HOTAIR has been observed to circulate within the bloodstream and possesses an integral epigenetic regulatory function in the transcriptional pathways of many diseases. Recent studies have suggested that HOTAIR offers promise as a biomarker for the detection and treatment of CVDs. The investigation on HOTAIR’s role in CVDs, however, is still in its early phases. The goal of the current study is to give a thorough overview of recent developments in the field of analyzing the molecular mechanism of HOTAIR in controlling the pathophysiological processes of CVDs as well as its possible therapeutic uses.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255007","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}

引用次数: 0

Cancer pharmacoinformatics: Databases and analytical tools 癌症药物信息学：数据库和分析工具

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-19 DOI: 10.1007/s10142-024-01445-5

Pradnya Kamble, Prinsa R. Nagar, Kaushikkumar A. Bhakhar, Prabha Garg, M. Elizabeth Sobhia, Srivatsava Naidu, Prasad V. Bharatam

{"title":"Cancer pharmacoinformatics: Databases and analytical tools","authors":"Pradnya Kamble, Prinsa R. Nagar, Kaushikkumar A. Bhakhar, Prabha Garg, M. Elizabeth Sobhia, Srivatsava Naidu, Prasad V. Bharatam","doi":"10.1007/s10142-024-01445-5","DOIUrl":"10.1007/s10142-024-01445-5","url":null,"abstract":"<div><p>Cancer is a subject of extensive investigation, and the utilization of omics technology has resulted in the generation of substantial volumes of big data in cancer research. Numerous databases are being developed to manage and organize this data effectively. These databases encompass various domains such as genomics, transcriptomics, proteomics, metabolomics, immunology, and drug discovery. The application of computational tools into various core components of pharmaceutical sciences constitutes \"Pharmacoinformatics\", an emerging paradigm in rational drug discovery. The three major features of pharmacoinformatics include (i) Structure modelling of putative drugs and targets, (ii) Compilation of databases and analysis using statistical approaches, and (iii) Employing artificial intelligence/machine learning algorithms for the discovery of novel therapeutic molecules. The development, updating, and analysis of databases using statistical approaches play a pivotal role in pharmacoinformatics. Multiple software tools are associated with oncoinformatics research. This review catalogs the databases and computational tools related to cancer drug discovery and highlights their potential implications in the pharmacoinformatics of cancer.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142254969","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}

引用次数: 0

Deciphering the role of FOXP4 in long COVID: exploring genetic associations, evolutionary conservation, and drug identification through bioinformatics analysis 解密 FOXP4 在长 COVID 中的作用：通过生物信息学分析探索遗传关联、进化保护和药物鉴定

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-19 DOI: 10.1007/s10142-024-01451-7

Manoj Kumar Gupta, Gayatri Gouda, Ramakrishna Vadde

{"title":"Deciphering the role of FOXP4 in long COVID: exploring genetic associations, evolutionary conservation, and drug identification through bioinformatics analysis","authors":"Manoj Kumar Gupta, Gayatri Gouda, Ramakrishna Vadde","doi":"10.1007/s10142-024-01451-7","DOIUrl":"10.1007/s10142-024-01451-7","url":null,"abstract":"<div><p>Long COVID (LC) refers to a condition characterized by a variety of lingering symptoms that persist for more than 4 to 12 weeks following the initial acute SARS-CoV-2 infection. Recent research has suggested that the <i>FOXP4</i> gene could potentially be a significant factor contributing to LC. Owing to that, this study investigates <i>FOXP4</i>’s role in LC by analyzing public datasets to understand its evolution and expression in diverse human populations and searching for drugs to reduce LC symptoms. Population genetic analysis of <i>FOXP4</i> across human populations unmasks distinct genetic diversity patterns and positive selection signatures, suggesting potential population-specific susceptibilities to conditions like LC. Further, we also observed that <i>FOXP4</i> experiences high expression during LC. To identify potential inhibitors, drug screening analysis identifies synthetic drugs like Glisoxepide, and natural compounds Kapurimycin A3 produced from <i>Streptomyces sp</i>, and Cucurbitacin B from <i>Begonia nantoensis</i> as promising candidates. Overall, our research contributes to understanding how<i> FOXP4</i> may serve as a therapeutic target for mitigating the impact of LC.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142254998","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}

引用次数: 0

C-FOS inhibition promotes pancreatic cancer cell ferroptosis by transcriptionally regulating the expression of SLC7A11 抑制 C-FOS 可通过转录调节 SLC7A11 的表达促进胰腺癌细胞的铁变态反应

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-18 DOI: 10.1007/s10142-024-01429-5

Shuangjia Wang, Hao Yu, Ping Guo, Liuxing Feng, Zhimin Li

{"title":"C-FOS inhibition promotes pancreatic cancer cell ferroptosis by transcriptionally regulating the expression of SLC7A11","authors":"Shuangjia Wang, Hao Yu, Ping Guo, Liuxing Feng, Zhimin Li","doi":"10.1007/s10142-024-01429-5","DOIUrl":"10.1007/s10142-024-01429-5","url":null,"abstract":"<div><p>Cellular proto-oncogene C-Fos forms the AP-1 transcription factor by dimerizing with proto-oncogene c-Jun; this factor upregulates the transcription of genes associated with different malignancies. However, its functions in pancreatic adenocarcinoma (PAAD) remain poorly understood. In this study, the c-Fos was increased in PAAD cells and tissues through bioinformatic analysis, RT-PCR, and WB. In two PAAD cell lines, PANC-1 and BxPC-3, we performed c-Fos knockdown studies using short hairpin RNA (shRNA). Functional analysis indicated that c-Fos depletion in PAAD cells inhibits cell proliferation and promotes ferroptosis. Chromatin Immunoprecipitation (ChIP) and Dual-luciferase experiments showed that c-Fos coupled to the promoter region of SLC7A11 stimulated its transcription, providing mechanistic insight into the process. Moreover, SLC7A11 blocked the decline of proliferation and ferroptosis by c-Fos knockdown in PAAD cells. Furthermore, a xenograft nude mouse model was established to study the impact of c-Fos on tumorigenesis in vivo. Depletion of c-Fos could suppress PC tumor growth and the expressions of SLC7A11, ki-67, and 4HNE, but overexpression of SLC7A11 reversed this process. In summary, our investigation has shown that c-Fos acts as a transcriptional regulator of SLC7A11, which may enhance tumour growth in pancreatic cancer by inhibiting ferroptosis. These results indicate that c-Fos might be a promising target for treating ferroptosis in PAAD.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255000","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}

引用次数: 0

Is the voltage-gated sodium channel β3 subunit (SCN3B) a biomarker for glioma? 电压门控钠通道β3亚基（SCN3B）是胶质瘤的生物标志物吗？

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-18 DOI: 10.1007/s10142-024-01443-7

Hengrui Liu, Jieling Weng, Christopher L.-H. Huang, Antony P. Jackson

{"title":"Is the voltage-gated sodium channel β3 subunit (SCN3B) a biomarker for glioma?","authors":"Hengrui Liu, Jieling Weng, Christopher L.-H. Huang, Antony P. Jackson","doi":"10.1007/s10142-024-01443-7","DOIUrl":"10.1007/s10142-024-01443-7","url":null,"abstract":"<div><p>Recent studies suggest a need for reliable biomarkers enhancing prognosis prediction and treatment strategies in cancer. Here, we performed a data analysis bearing on the expression of SCN3B, voltage-gated sodium channel (VGSC) β3 subunit, as a possible candidate for the development of a glioma biomarker for the first time. This extends our previous review article that mentioned the potential of SCN3B as a prognostic biomarker for glioma survival, further examining its association with existing indicators and immune responses. We utilized clinical and genomic data from multiple glioma cohorts. These include the Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA). We employed analytical techniques including time-dependent receiver operating characteristic (ROC) analysis, decision curves analysis (DCA), and correlation studies with immune checkpoint markers. Our findings indicate a differential SCN3B expression between glioma grades, and that this significantly correlates with patient survival, particularly in oligodendroglioma subtypes. The DCA curves suggested that the inclusion of SCN3B in the prognostic model would improve decision-making in these subtypes. Moreover, SCN3B expression positively correlated with the presence of key immune cells and negatively correlated with several immune checkpoint inhibitors. This suggests potential roles in modulating immune responses in glioma. Thus, SCN3B emerges as a promising potential prognostic biomarker for glioma, especially for oligodendroglioma. Its dual correlations with prognosis and immune regulation present a compelling case for further experimental and clinical investigations to establish its utility in enhancing glioma management strategies. These findings underscore the importance of integrating novel biomarkers with traditional prognostic models to refine treatment paradigms and improve patient outcomes.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142254999","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}

引用次数: 0