Next Generation Sequencing for Long Non-coding RNAs Profile for CD4+ T Cells in the Mouse Model of Acute Asthma
Background and AimsAlthough long non-coding RNAs (lncRNAs) have been linked to many diseases including asthma, little is known about lncRNA transcriptomes of CD4+ T cells in asthma. The present study aimed to explore the lncRNAs profile in the CD4+T cells from the mouse model of acute asthma.Methods...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-06-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.00545/full |
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| author | Zhengxia Wang Ningfei Ji Zhongqi Chen Chaojie Wu Zhixiao Sun Wenqin Yu Wenqin Yu Fan Hu Mao Huang Mingshun Zhang Mingshun Zhang |
| author_facet | Zhengxia Wang Ningfei Ji Zhongqi Chen Chaojie Wu Zhixiao Sun Wenqin Yu Wenqin Yu Fan Hu Mao Huang Mingshun Zhang Mingshun Zhang |
| author_sort | Zhengxia Wang |
| collection | DOAJ |
| description | Background and AimsAlthough long non-coding RNAs (lncRNAs) have been linked to many diseases including asthma, little is known about lncRNA transcriptomes of CD4+ T cells in asthma. The present study aimed to explore the lncRNAs profile in the CD4+T cells from the mouse model of acute asthma.MethodsNext generation sequencing for lncRNAs and mRNAs was performed on CD4+ T cells from asthma and control mice. Gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were performed to predict the functions and signal pathways for the aberrant lncRNAs. The selected lncRNAs were further measured using quantitative real-time PCR (polymerase chain reaction) and observed in the fluorescence in situ hybridization (FISH). The lncRNA–mRNA co-expression network was constructed via Pearson’s correlation coefficient and Cytoscape 3.6.ResultsNext generation sequencing revealed 36 up-regulated lncRNAs and 98 down-regulated lncRNAs in acute asthma compared with controls. KEGG pathway analysis showed that cytokine-cytokine receptor interaction had the highest enrichment scores. A co-expression network was constructed in which 23 lncRNAs and 301 mRNAs altered formed a total of 12424 lncRNA and mRNA pairs. To validate the RNA sequencing results, we measured the 4 different lncRNAs using qPCR. The lncRNA fantom3_9230106C11 was significantly reduced in CD4+ T cells of asthma. Bioinformatics analysis showed that lncRNA fantom3_9230106C11 had the potential to interact with many miRNAs and transcription factors related to Th2 differentiation.ConclusionThis study provided the first evidence for different expression of lncRNAs of CD4+T cells in asthma and may serve as a template for further, larger functional in-depth analyses regarding asthma molecular lncRNAs. |
| first_indexed | 2024-12-14T19:51:48Z |
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| id | doaj.art-41ebdc1935f6452c8fb3b6c3ade1c6ed |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-14T19:51:48Z |
| publishDate | 2019-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-41ebdc1935f6452c8fb3b6c3ade1c6ed2022-12-21T22:49:23ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-06-011010.3389/fgene.2019.00545452707Next Generation Sequencing for Long Non-coding RNAs Profile for CD4+ T Cells in the Mouse Model of Acute AsthmaZhengxia Wang0Ningfei Ji1Zhongqi Chen2Chaojie Wu3Zhixiao Sun4Wenqin Yu5Wenqin Yu6Fan Hu7Mao Huang8Mingshun Zhang9Mingshun Zhang10Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaDepartment of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaDepartment of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaDepartment of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaDepartment of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaDepartment of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaDepartment of Infectious Disease, Taizhou People’s Hospital, Taizhou, ChinaState Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, ChinaDepartment of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaNHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, ChinaDepartment of Immunology, Nanjing Medical University, Nanjing, ChinaBackground and AimsAlthough long non-coding RNAs (lncRNAs) have been linked to many diseases including asthma, little is known about lncRNA transcriptomes of CD4+ T cells in asthma. The present study aimed to explore the lncRNAs profile in the CD4+T cells from the mouse model of acute asthma.MethodsNext generation sequencing for lncRNAs and mRNAs was performed on CD4+ T cells from asthma and control mice. Gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were performed to predict the functions and signal pathways for the aberrant lncRNAs. The selected lncRNAs were further measured using quantitative real-time PCR (polymerase chain reaction) and observed in the fluorescence in situ hybridization (FISH). The lncRNA–mRNA co-expression network was constructed via Pearson’s correlation coefficient and Cytoscape 3.6.ResultsNext generation sequencing revealed 36 up-regulated lncRNAs and 98 down-regulated lncRNAs in acute asthma compared with controls. KEGG pathway analysis showed that cytokine-cytokine receptor interaction had the highest enrichment scores. A co-expression network was constructed in which 23 lncRNAs and 301 mRNAs altered formed a total of 12424 lncRNA and mRNA pairs. To validate the RNA sequencing results, we measured the 4 different lncRNAs using qPCR. The lncRNA fantom3_9230106C11 was significantly reduced in CD4+ T cells of asthma. Bioinformatics analysis showed that lncRNA fantom3_9230106C11 had the potential to interact with many miRNAs and transcription factors related to Th2 differentiation.ConclusionThis study provided the first evidence for different expression of lncRNAs of CD4+T cells in asthma and may serve as a template for further, larger functional in-depth analyses regarding asthma molecular lncRNAs.https://www.frontiersin.org/article/10.3389/fgene.2019.00545/fullasthmaCD4+ T lymphocytelong non-coding RNAmRNAnext-generation sequencing |
| spellingShingle | Zhengxia Wang Ningfei Ji Zhongqi Chen Chaojie Wu Zhixiao Sun Wenqin Yu Wenqin Yu Fan Hu Mao Huang Mingshun Zhang Mingshun Zhang Next Generation Sequencing for Long Non-coding RNAs Profile for CD4+ T Cells in the Mouse Model of Acute Asthma Frontiers in Genetics asthma CD4+ T lymphocyte long non-coding RNA mRNA next-generation sequencing |
| title | Next Generation Sequencing for Long Non-coding RNAs Profile for CD4+ T Cells in the Mouse Model of Acute Asthma |
| title_full | Next Generation Sequencing for Long Non-coding RNAs Profile for CD4+ T Cells in the Mouse Model of Acute Asthma |
| title_fullStr | Next Generation Sequencing for Long Non-coding RNAs Profile for CD4+ T Cells in the Mouse Model of Acute Asthma |
| title_full_unstemmed | Next Generation Sequencing for Long Non-coding RNAs Profile for CD4+ T Cells in the Mouse Model of Acute Asthma |
| title_short | Next Generation Sequencing for Long Non-coding RNAs Profile for CD4+ T Cells in the Mouse Model of Acute Asthma |
| title_sort | next generation sequencing for long non coding rnas profile for cd4 t cells in the mouse model of acute asthma |
| topic | asthma CD4+ T lymphocyte long non-coding RNA mRNA next-generation sequencing |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.00545/full |
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