{"title":"直肠癌相关lncRNA-mRNA ceRNA网络的构建和表征揭示了直肠癌预后的生物标志物","authors":"Guoying Cai, Meifei Sun, Xinrong Li, Junquan Zhu","doi":"10.1049/syb2.12035","DOIUrl":null,"url":null,"abstract":"<p>Rectal cancer is an important cause of cancer-related deaths worldwide. In this study, the differentially expressed (DE) lncRNAs/mRNAs were first identified and the correlation level between DE lncRNAs and mRNAs were calculated. The results showed that genes of highly correlated lncRNA-mRNA pairs presented strong prognosis effects, such as <i>GPM6A</i>, <i>METTL24</i>, <i>SCN7A</i>, <i>HAND2-AS1</i> and <i>PDZRN4</i>. Then, the rectal cancer-related lncRNA-mRNA network was constructed based on the ceRNA theory. Topological analysis of the network revealed that the network was maintained by hub nodes and a hub subnetwork was constructed, including the hub lncRNA MIR143HG and MBNL1-SA1. Further analysis indicated that the hub subnetwork was highly related to cancer pathways, such as ‘Focal adhesion’ and ‘Wnt signalling pathway’. Hub subnetwork also had significant prognosis capability. A closed lncRNA-mRNA module was identified by bilateral network clustering. Genes in modules also showed high prognosis effects. Finally, a core lncRNA-TF crosstalk network was identified to uncover the crosstalk and regulatory mechanisms of lncRNAs and TFs by integrating ceRNA crosstalks and TF binding affinities. Some core genes, such as MEIS1, GLI3 and HAND2-AS1 were considered as the key regulators in tumourigenesis. Based on the authors’ comprehensive analysis, all these lncRNA-mRNA crosstalks provided promising clues for biological prognosis of rectal cancer.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"15 6","pages":"192-204"},"PeriodicalIF":1.9000,"publicationDate":"2021-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8675822/pdf/","citationCount":"5","resultStr":"{\"title\":\"Construction and characterization of rectal cancer-related lncRNA-mRNA ceRNA network reveals prognostic biomarkers in rectal cancer\",\"authors\":\"Guoying Cai, Meifei Sun, Xinrong Li, Junquan Zhu\",\"doi\":\"10.1049/syb2.12035\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>Rectal cancer is an important cause of cancer-related deaths worldwide. In this study, the differentially expressed (DE) lncRNAs/mRNAs were first identified and the correlation level between DE lncRNAs and mRNAs were calculated. The results showed that genes of highly correlated lncRNA-mRNA pairs presented strong prognosis effects, such as <i>GPM6A</i>, <i>METTL24</i>, <i>SCN7A</i>, <i>HAND2-AS1</i> and <i>PDZRN4</i>. Then, the rectal cancer-related lncRNA-mRNA network was constructed based on the ceRNA theory. Topological analysis of the network revealed that the network was maintained by hub nodes and a hub subnetwork was constructed, including the hub lncRNA MIR143HG and MBNL1-SA1. Further analysis indicated that the hub subnetwork was highly related to cancer pathways, such as ‘Focal adhesion’ and ‘Wnt signalling pathway’. Hub subnetwork also had significant prognosis capability. A closed lncRNA-mRNA module was identified by bilateral network clustering. Genes in modules also showed high prognosis effects. Finally, a core lncRNA-TF crosstalk network was identified to uncover the crosstalk and regulatory mechanisms of lncRNAs and TFs by integrating ceRNA crosstalks and TF binding affinities. Some core genes, such as MEIS1, GLI3 and HAND2-AS1 were considered as the key regulators in tumourigenesis. Based on the authors’ comprehensive analysis, all these lncRNA-mRNA crosstalks provided promising clues for biological prognosis of rectal cancer.</p>\",\"PeriodicalId\":50379,\"journal\":{\"name\":\"IET Systems Biology\",\"volume\":\"15 6\",\"pages\":\"192-204\"},\"PeriodicalIF\":1.9000,\"publicationDate\":\"2021-10-06\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8675822/pdf/\",\"citationCount\":\"5\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"IET Systems Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1049/syb2.12035\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"CELL BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"IET Systems Biology","FirstCategoryId":"99","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1049/syb2.12035","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"CELL BIOLOGY","Score":null,"Total":0}
Construction and characterization of rectal cancer-related lncRNA-mRNA ceRNA network reveals prognostic biomarkers in rectal cancer
Rectal cancer is an important cause of cancer-related deaths worldwide. In this study, the differentially expressed (DE) lncRNAs/mRNAs were first identified and the correlation level between DE lncRNAs and mRNAs were calculated. The results showed that genes of highly correlated lncRNA-mRNA pairs presented strong prognosis effects, such as GPM6A, METTL24, SCN7A, HAND2-AS1 and PDZRN4. Then, the rectal cancer-related lncRNA-mRNA network was constructed based on the ceRNA theory. Topological analysis of the network revealed that the network was maintained by hub nodes and a hub subnetwork was constructed, including the hub lncRNA MIR143HG and MBNL1-SA1. Further analysis indicated that the hub subnetwork was highly related to cancer pathways, such as ‘Focal adhesion’ and ‘Wnt signalling pathway’. Hub subnetwork also had significant prognosis capability. A closed lncRNA-mRNA module was identified by bilateral network clustering. Genes in modules also showed high prognosis effects. Finally, a core lncRNA-TF crosstalk network was identified to uncover the crosstalk and regulatory mechanisms of lncRNAs and TFs by integrating ceRNA crosstalks and TF binding affinities. Some core genes, such as MEIS1, GLI3 and HAND2-AS1 were considered as the key regulators in tumourigenesis. Based on the authors’ comprehensive analysis, all these lncRNA-mRNA crosstalks provided promising clues for biological prognosis of rectal cancer.
期刊介绍：
IET Systems Biology covers intra- and inter-cellular dynamics, using systems- and signal-oriented approaches. Papers that analyse genomic data in order to identify variables and basic relationships between them are considered if the results provide a basis for mathematical modelling and simulation of cellular dynamics. Manuscripts on molecular and cell biological studies are encouraged if the aim is a systems approach to dynamic interactions within and between cells.
The scope includes the following topics:
Genomics, transcriptomics, proteomics, metabolomics, cells, tissue and the physiome; molecular and cellular interaction, gene, cell and protein function; networks and pathways; metabolism and cell signalling; dynamics, regulation and control; systems, signals, and information; experimental data analysis; mathematical modelling, simulation and theoretical analysis; biological modelling, simulation, prediction and control; methodologies, databases, tools and algorithms for modelling and simulation; modelling, analysis and control of biological networks; synthetic biology and bioengineering based on systems biology.
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