DoxoDB: A Database for the Expression Analysis of Doxorubicin-Induced lncRNA Genes.

IF 3.6 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Non-Coding RNA Pub Date : 2023-07-13 DOI:10.3390/ncrna9040039

Rebecca Distefano, Mirolyuba Ilieva, Jens Hedelund Madsen, Sarah Rennie, Shizuka Uchida

{"title":"DoxoDB: A Database for the Expression Analysis of Doxorubicin-Induced lncRNA Genes.","authors":"Rebecca Distefano, Mirolyuba Ilieva, Jens Hedelund Madsen, Sarah Rennie, Shizuka Uchida","doi":"10.3390/ncrna9040039","DOIUrl":null,"url":null,"abstract":"Cancer and cardiovascular disease are the leading causes of death worldwide. Recent evidence suggests that these two life-threatening diseases share several features in disease progression, such as angiogenesis, fibrosis, and immune responses. This has led to the emergence of a new field called cardio-oncology. Doxorubicin is a chemotherapy drug widely used to treat cancer, such as bladder and breast cancer. However, this drug causes serious side effects, including acute ventricular dysfunction, cardiomyopathy, and heart failure. Based on this evidence, we hypothesize that comparing the expression profiles of cells and tissues treated with doxorubicin may yield new insights into the adverse effects of the drug on cellular activities. To test this hypothesis, we analyzed published RNA sequencing (RNA-seq) data from doxorubicin-treated cells to identify commonly differentially expressed genes, including long non-coding RNAs (lncRNAs) as they are known to be dysregulated in diseased tissues and cells. From our systematic analysis, we identified several doxorubicin-induced genes. To confirm these findings, we treated human cardiac fibroblasts with doxorubicin to record expression changes in the selected doxorubicin-induced genes and performed a loss-of-function experiment of the lncRNA MAP3K4-AS1. To further disseminate the analyzed data, we built the web database DoxoDB.","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":null,"pages":null},"PeriodicalIF":3.6000,"publicationDate":"2023-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10366827/pdf/","citationCount":"2","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Non-Coding RNA","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3390/ncrna9040039","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}

引用次数: 2

Abstract

Cancer and cardiovascular disease are the leading causes of death worldwide. Recent evidence suggests that these two life-threatening diseases share several features in disease progression, such as angiogenesis, fibrosis, and immune responses. This has led to the emergence of a new field called cardio-oncology. Doxorubicin is a chemotherapy drug widely used to treat cancer, such as bladder and breast cancer. However, this drug causes serious side effects, including acute ventricular dysfunction, cardiomyopathy, and heart failure. Based on this evidence, we hypothesize that comparing the expression profiles of cells and tissues treated with doxorubicin may yield new insights into the adverse effects of the drug on cellular activities. To test this hypothesis, we analyzed published RNA sequencing (RNA-seq) data from doxorubicin-treated cells to identify commonly differentially expressed genes, including long non-coding RNAs (lncRNAs) as they are known to be dysregulated in diseased tissues and cells. From our systematic analysis, we identified several doxorubicin-induced genes. To confirm these findings, we treated human cardiac fibroblasts with doxorubicin to record expression changes in the selected doxorubicin-induced genes and performed a loss-of-function experiment of the lncRNA MAP3K4-AS1. To further disseminate the analyzed data, we built the web database DoxoDB.

Abstract Image

查看原文本刊更多论文

DoxoDB:多柔比星诱导的lncRNA基因表达分析数据库。

癌症和心血管疾病是全世界的主要死亡原因。最近的证据表明，这两种危及生命的疾病在疾病进展中有几个共同的特征，如血管生成、纤维化和免疫反应。这导致了一个叫做心脏肿瘤学的新领域的出现。阿霉素是一种化疗药物，广泛用于治疗癌症，如膀胱癌和乳腺癌。然而，这种药物会引起严重的副作用，包括急性心室功能障碍、心肌病和心力衰竭。基于这一证据，我们假设比较阿霉素处理的细胞和组织的表达谱可能会对药物对细胞活动的不良影响产生新的见解。为了验证这一假设，我们分析了已发表的来自阿霉素处理细胞的RNA测序(RNA-seq)数据，以鉴定常见的差异表达基因，包括长链非编码RNA (lncRNAs)，因为它们已知在病变组织和细胞中失调。从我们的系统分析中，我们确定了几个阿霉素诱导的基因。为了证实这些发现，我们用阿霉素处理人类心脏成纤维细胞，记录了阿霉素诱导的基因表达变化，并进行了lncRNA MAP3K4-AS1的功能缺失实验。为了进一步传播分析数据，我们构建了web数据库DoxoDB。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Non-Coding RNA Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

6.70

自引率

4.70%

发文量

审稿时长

10 weeks

期刊介绍： Functional studies dealing with identification, structure-function relationships or biological activity of: small regulatory RNAs (miRNAs, siRNAs and piRNAs) associated with the RNA interference pathway small nuclear RNAs, small nucleolar and tRNAs derived small RNAs other types of small RNAs, such as those associated with splice junctions and transcription start sites long non-coding RNAs, including antisense RNAs, long ''intergenic'' RNAs, intronic RNAs and ''enhancer'' RNAs other classes of RNAs such as vault RNAs, scaRNAs, circular RNAs, 7SL RNAs, telomeric and centromeric RNAs regulatory functions of mRNAs and UTR-derived RNAs catalytic and allosteric (riboswitch) RNAs viral, transposon and repeat-derived RNAs bacterial regulatory RNAs, including CRISPR RNAS Analysis of RNA processing, RNA binding proteins, RNA signaling and RNA interaction pathways: DICER AGO, PIWI and PIWI-like proteins other classes of RNA binding and RNA transport proteins RNA interactions with chromatin-modifying complexes RNA interactions with DNA and other RNAs the role of RNA in the formation and function of specialized subnuclear organelles and other aspects of cell biology intercellular and intergenerational RNA signaling RNA processing structure-function relationships in RNA complexes RNA analyses, informatics, tools and technologies: transcriptomic analyses and technologies development of tools and technologies for RNA biology and therapeutics Translational studies involving long and short non-coding RNAs: identification of biomarkers development of new therapies involving microRNAs and other ncRNAs clinical studies involving microRNAs and other ncRNAs.