Insight into the lncRNA–mRNA Co-Expression Profile and ceRNA Network in Lipopolysaccharide-Induced Acute Lung Injury
Long non-coding RNAs (lncRNAs) participate in acute lung injury (ALI). However, their latent biological function and molecular mechanism have not been fully understood. In the present study, the global expression profiles of lncRNAs and mRNAs between the control and lipopolysaccharide (LPS)-stimulat...
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| Format: | Article |
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MDPI AG
2023-07-01
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| Series: | Current Issues in Molecular Biology |
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| Online Access: | https://www.mdpi.com/1467-3045/45/7/389 |
| _version_ | 1797589707621662720 |
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| author | Yue Shen Linjing Gong Fan Xu Sijiao Wang Hanhan Liu Yali Wang Lijuan Hu Lei Zhu |
| author_facet | Yue Shen Linjing Gong Fan Xu Sijiao Wang Hanhan Liu Yali Wang Lijuan Hu Lei Zhu |
| author_sort | Yue Shen |
| collection | DOAJ |
| description | Long non-coding RNAs (lncRNAs) participate in acute lung injury (ALI). However, their latent biological function and molecular mechanism have not been fully understood. In the present study, the global expression profiles of lncRNAs and mRNAs between the control and lipopolysaccharide (LPS)-stimulated groups of human normal lung epithelial cells (BEAS-2B) were determined using high-throughput sequencing. Overall, a total of 433 lncRNAs and 183 mRNAs were differentially expressed. A lncRNA–mRNA co-expression network was established, and then the top 10 lncRNAs were screened using topological methods. <i>Gene Ontology</i> and <i>Kyoto Encyclopedia of Genes and Genomes</i> analysis results showed that the key lncRNAs targeting mRNAs were mostly enriched in the inflammatory-related biological processes. Gene set variation analysis and Pearson’s correlation coefficients confirmed the close correlation for the top 10 lncRNAs with inflammatory responses. A protein–protein interaction network analysis was conducted based on the key lncRNAs targeting mRNAs, where IL-1β, IL-6, and CXCL8 were regarded as the hub genes. A competing endogenous RNA (ceRNA) modulatory network was created with five lncRNAs, thirteen microRNAs, and twelve mRNAs. Finally, real-time quantitative reverse transcription-polymerase chain reaction was employed to verify the expression levels of several key lncRNAs in BEAS-2B cells and human serum samples. |
| first_indexed | 2024-03-11T01:10:23Z |
| format | Article |
| id | doaj.art-158b9cec855441ac8005cfc22af22f32 |
| institution | Directory Open Access Journal |
| issn | 1467-3037 1467-3045 |
| language | English |
| last_indexed | 2024-03-11T01:10:23Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Current Issues in Molecular Biology |
| spelling | doaj.art-158b9cec855441ac8005cfc22af22f322023-11-18T18:51:34ZengMDPI AGCurrent Issues in Molecular Biology1467-30371467-30452023-07-014576170618910.3390/cimb45070389Insight into the lncRNA–mRNA Co-Expression Profile and ceRNA Network in Lipopolysaccharide-Induced Acute Lung InjuryYue Shen0Linjing Gong1Fan Xu2Sijiao Wang3Hanhan Liu4Yali Wang5Lijuan Hu6Lei Zhu7Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaDepartment of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, ChinaDepartment of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaDepartment of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaDepartment of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaDepartment of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaDepartment of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaDepartment of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaLong non-coding RNAs (lncRNAs) participate in acute lung injury (ALI). However, their latent biological function and molecular mechanism have not been fully understood. In the present study, the global expression profiles of lncRNAs and mRNAs between the control and lipopolysaccharide (LPS)-stimulated groups of human normal lung epithelial cells (BEAS-2B) were determined using high-throughput sequencing. Overall, a total of 433 lncRNAs and 183 mRNAs were differentially expressed. A lncRNA–mRNA co-expression network was established, and then the top 10 lncRNAs were screened using topological methods. <i>Gene Ontology</i> and <i>Kyoto Encyclopedia of Genes and Genomes</i> analysis results showed that the key lncRNAs targeting mRNAs were mostly enriched in the inflammatory-related biological processes. Gene set variation analysis and Pearson’s correlation coefficients confirmed the close correlation for the top 10 lncRNAs with inflammatory responses. A protein–protein interaction network analysis was conducted based on the key lncRNAs targeting mRNAs, where IL-1β, IL-6, and CXCL8 were regarded as the hub genes. A competing endogenous RNA (ceRNA) modulatory network was created with five lncRNAs, thirteen microRNAs, and twelve mRNAs. Finally, real-time quantitative reverse transcription-polymerase chain reaction was employed to verify the expression levels of several key lncRNAs in BEAS-2B cells and human serum samples.https://www.mdpi.com/1467-3045/45/7/389acute lung injurylong noncoding RNAshigh-throughput RNA sequencingexpression profileceRNA regulatory networkinflammatory response |
| spellingShingle | Yue Shen Linjing Gong Fan Xu Sijiao Wang Hanhan Liu Yali Wang Lijuan Hu Lei Zhu Insight into the lncRNA–mRNA Co-Expression Profile and ceRNA Network in Lipopolysaccharide-Induced Acute Lung Injury Current Issues in Molecular Biology acute lung injury long noncoding RNAs high-throughput RNA sequencing expression profile ceRNA regulatory network inflammatory response |
| title | Insight into the lncRNA–mRNA Co-Expression Profile and ceRNA Network in Lipopolysaccharide-Induced Acute Lung Injury |
| title_full | Insight into the lncRNA–mRNA Co-Expression Profile and ceRNA Network in Lipopolysaccharide-Induced Acute Lung Injury |
| title_fullStr | Insight into the lncRNA–mRNA Co-Expression Profile and ceRNA Network in Lipopolysaccharide-Induced Acute Lung Injury |
| title_full_unstemmed | Insight into the lncRNA–mRNA Co-Expression Profile and ceRNA Network in Lipopolysaccharide-Induced Acute Lung Injury |
| title_short | Insight into the lncRNA–mRNA Co-Expression Profile and ceRNA Network in Lipopolysaccharide-Induced Acute Lung Injury |
| title_sort | insight into the lncrna mrna co expression profile and cerna network in lipopolysaccharide induced acute lung injury |
| topic | acute lung injury long noncoding RNAs high-throughput RNA sequencing expression profile ceRNA regulatory network inflammatory response |
| url | https://www.mdpi.com/1467-3045/45/7/389 |
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