{"title":"利用疾病相关lncRNA-mRNA通路网络分析杜氏肌营养不良的长链非编码rna相关调控机制","authors":"Bing Xu, Chunlei Zheng","doi":"10.1155/2022/8548804","DOIUrl":null,"url":null,"abstract":"<p><strong>Objective: </strong>This study aimed to investigate the molecular regulatory mechanisms underpinning Duchenne muscular dystrophy (DMD).</p><p><strong>Methods: </strong>Using microarray data, differentially expressed long noncoding RNAs (DELs) and DMD-related differentially expressed mRNAs (DEMs) were screened based on the comparative toxicogenomics database, using a cutoff of |log<sub>2</sub> fold change| > 1 and false discovery rate (FDR) < 0.05. Then, protein-protein interaction (PPI), coexpression network of lncRNA-mRNA, and DMD-related lncRNA-mRNA pathway networks were constructed, and functional analyses of the genes in the network were performed. Finally, the proportions of immune cells infiltrating the muscle tissues in DMD were analyzed, and the correlation between the immune cells and expression of the DELs/DEMs was studied.</p><p><strong>Results: </strong>A total of 46 DELs and 313 DMD-related DEMs were identified. The PPI network revealed <i>STAT1</i>, <i>VEGFA</i>, and <i>CCL2</i> to be the top three hub genes. The DMD-related lncRNA-mRNA pathway network comprising two pathways, nine DELs, and nine DMD-related DEMs showed that <i>PYCARD</i>, <i>RIPK2</i>, and <i>CASP1</i> were significantly enriched in the NOD-like receptor signaling pathway, whereas <i>MAP2K2</i>, <i>LUM</i>, <i>RPS6</i>, <i>PDCD4</i>, <i>TWIST1</i>, and <i>HIF1A</i> were significantly enriched with proteoglycans in cancers. The nine DELs in this network were DBET, MBNL1-AS1, MIR29B2CHG, CCDC18-AS1, FAM111A-DT, GAS5, LINC01290, ATP2B1-AS1, and PSMB8-AS1.</p><p><strong>Conclusion: </strong>The nine DMD-related DEMs and DELs identified in this study may play important roles in the occurrence and progression of DMD through the two pathways of the NOD-like receptor signaling pathway and proteoglycans in cancers.</p>","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":"2022 ","pages":"8548804"},"PeriodicalIF":1.4000,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9771664/pdf/","citationCount":"0","resultStr":"{\"title\":\"Analysis of Long Noncoding RNAs-Related Regulatory Mechanisms in Duchenne Muscular Dystrophy Using a Disease-Related lncRNA-mRNA Pathway Network.\",\"authors\":\"Bing Xu, Chunlei Zheng\",\"doi\":\"10.1155/2022/8548804\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Objective: </strong>This study aimed to investigate the molecular regulatory mechanisms underpinning Duchenne muscular dystrophy (DMD).</p><p><strong>Methods: </strong>Using microarray data, differentially expressed long noncoding RNAs (DELs) and DMD-related differentially expressed mRNAs (DEMs) were screened based on the comparative toxicogenomics database, using a cutoff of |log<sub>2</sub> fold change| > 1 and false discovery rate (FDR) < 0.05. Then, protein-protein interaction (PPI), coexpression network of lncRNA-mRNA, and DMD-related lncRNA-mRNA pathway networks were constructed, and functional analyses of the genes in the network were performed. Finally, the proportions of immune cells infiltrating the muscle tissues in DMD were analyzed, and the correlation between the immune cells and expression of the DELs/DEMs was studied.</p><p><strong>Results: </strong>A total of 46 DELs and 313 DMD-related DEMs were identified. The PPI network revealed <i>STAT1</i>, <i>VEGFA</i>, and <i>CCL2</i> to be the top three hub genes. The DMD-related lncRNA-mRNA pathway network comprising two pathways, nine DELs, and nine DMD-related DEMs showed that <i>PYCARD</i>, <i>RIPK2</i>, and <i>CASP1</i> were significantly enriched in the NOD-like receptor signaling pathway, whereas <i>MAP2K2</i>, <i>LUM</i>, <i>RPS6</i>, <i>PDCD4</i>, <i>TWIST1</i>, and <i>HIF1A</i> were significantly enriched with proteoglycans in cancers. The nine DELs in this network were DBET, MBNL1-AS1, MIR29B2CHG, CCDC18-AS1, FAM111A-DT, GAS5, LINC01290, ATP2B1-AS1, and PSMB8-AS1.</p><p><strong>Conclusion: </strong>The nine DMD-related DEMs and DELs identified in this study may play important roles in the occurrence and progression of DMD through the two pathways of the NOD-like receptor signaling pathway and proteoglycans in cancers.</p>\",\"PeriodicalId\":12778,\"journal\":{\"name\":\"Genetics research\",\"volume\":\"2022 \",\"pages\":\"8548804\"},\"PeriodicalIF\":1.4000,\"publicationDate\":\"2022-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9771664/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genetics research\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1155/2022/8548804\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genetics research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1155/2022/8548804","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
Analysis of Long Noncoding RNAs-Related Regulatory Mechanisms in Duchenne Muscular Dystrophy Using a Disease-Related lncRNA-mRNA Pathway Network.
Objective: This study aimed to investigate the molecular regulatory mechanisms underpinning Duchenne muscular dystrophy (DMD).
Methods: Using microarray data, differentially expressed long noncoding RNAs (DELs) and DMD-related differentially expressed mRNAs (DEMs) were screened based on the comparative toxicogenomics database, using a cutoff of |log2 fold change| > 1 and false discovery rate (FDR) < 0.05. Then, protein-protein interaction (PPI), coexpression network of lncRNA-mRNA, and DMD-related lncRNA-mRNA pathway networks were constructed, and functional analyses of the genes in the network were performed. Finally, the proportions of immune cells infiltrating the muscle tissues in DMD were analyzed, and the correlation between the immune cells and expression of the DELs/DEMs was studied.
Results: A total of 46 DELs and 313 DMD-related DEMs were identified. The PPI network revealed STAT1, VEGFA, and CCL2 to be the top three hub genes. The DMD-related lncRNA-mRNA pathway network comprising two pathways, nine DELs, and nine DMD-related DEMs showed that PYCARD, RIPK2, and CASP1 were significantly enriched in the NOD-like receptor signaling pathway, whereas MAP2K2, LUM, RPS6, PDCD4, TWIST1, and HIF1A were significantly enriched with proteoglycans in cancers. The nine DELs in this network were DBET, MBNL1-AS1, MIR29B2CHG, CCDC18-AS1, FAM111A-DT, GAS5, LINC01290, ATP2B1-AS1, and PSMB8-AS1.
Conclusion: The nine DMD-related DEMs and DELs identified in this study may play important roles in the occurrence and progression of DMD through the two pathways of the NOD-like receptor signaling pathway and proteoglycans in cancers.
期刊介绍：
Genetics Research is a key forum for original research on all aspects of human and animal genetics, reporting key findings on genomes, genes, mutations and molecular interactions, extending out to developmental, evolutionary, and population genetics as well as ethical, legal and social aspects. Our aim is to lead to a better understanding of genetic processes in health and disease. The journal focuses on the use of new technologies, such as next generation sequencing together with bioinformatics analysis, to produce increasingly detailed views of how genes function in tissues and how these genes perform, individually or collectively, in normal development and disease aetiology. The journal publishes original work, review articles, short papers, computational studies, and novel methods and techniques in research covering humans and well-established genetic organisms. Key subject areas include medical genetics, genomics, human evolutionary and population genetics, bioinformatics, genetics of complex traits, molecular and developmental genetics, Evo-Devo, quantitative and statistical genetics, behavioural genetics and environmental genetics. The breadth and quality of research make the journal an invaluable resource for medical geneticists, molecular biologists, bioinformaticians and researchers involved in genetic basis of diseases, evolutionary and developmental studies.
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