Whole transcriptome analysis reveals that immune infiltration- lncRNAs are related to cellular apoptosis in liver transplantation
IntroductionIn most instances, liver transplantation (LT) is the only available treatment for end‐stage liver diseases. However, LT could also induce serious liver diseases or injury, and the underlying mechanisms of LT-induced complications remain largely unknown, especially the mechanisms of the d...
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| Format: | Article |
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Frontiers Media S.A.
2023-04-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1152742/full |
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| author | Shile Wu Shile Wu Chao Cheng Wenjun Zhu Jinyu Yang Bei-bei He Song Li Xinsheng Wang Hao Guo Dong Chen Ya-min Guo |
| author_facet | Shile Wu Shile Wu Chao Cheng Wenjun Zhu Jinyu Yang Bei-bei He Song Li Xinsheng Wang Hao Guo Dong Chen Ya-min Guo |
| author_sort | Shile Wu |
| collection | DOAJ |
| description | IntroductionIn most instances, liver transplantation (LT) is the only available treatment for end‐stage liver diseases. However, LT could also induce serious liver diseases or injury, and the underlying mechanisms of LT-induced complications remain largely unknown, especially the mechanisms of the dysfunction of the immune system mediated by long noncoding RNAs (lncRNAs).MethodsIn this study, we globally analyzed the proportion of immune cells by using the transcriptome sequencing data (RNA-seq) of needle-core liver biopsies from pre- and post-transplantation recipients. Dysregulated lncRNAs were found to be correlated with the altered fractions of immune cells. We finally explored the potential targets of dysregulated lncRNAs and analyzed their functions in LT.ResultsWe found that in the samples, some immune cells changed significantly after LT, including CD4 T cells, NK cells and mast cells. The proportion of macrophages in different polarization states also changed significantly, with M0 macrophages increasing and M2 macrophages decreasing. Through weighted gene co-expression network analysis (WGCNA), 7 gene expression modules related to LT were identified. These modules were related to changes in the proportion of different immune cells. The functions of these modules represent the response modes of different functional genes after LT. Among these modules, MEtan and MEyellow modules were primarily enriched in apoptosis and inflammatory pathways. Twelve immunity-related lncRNAs were identified for the first time, and the regulatory network co-changing with immune cells was also identified. The co-expressed genes of these lncRNAs were highly enriched in apoptosis-related pathways. Many apoptosis-related genes were found to be up-regulated after LT.DiscussionIn summary, we speculated that the expression and regulation of these apoptotic genes may be related to the changes in the proportion of immune cells. Some of these lncRNAs and apoptosis-related genes have been reported to be related to cell proliferation and apoptosis. They are also potential biomarkers or therapeutic targets. |
| first_indexed | 2024-04-09T19:42:07Z |
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| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-09T19:42:07Z |
| publishDate | 2023-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-745843f942f04e8aa523d47a54e06ed92023-04-04T05:01:43ZengFrontiers Media S.A.Frontiers in Immunology1664-32242023-04-011410.3389/fimmu.2023.11527421152742Whole transcriptome analysis reveals that immune infiltration- lncRNAs are related to cellular apoptosis in liver transplantationShile Wu0Shile Wu1Chao Cheng2Wenjun Zhu3Jinyu Yang4Bei-bei He5Song Li6Xinsheng Wang7Hao Guo8Dong Chen9Ya-min Guo10Soochow University, Suzhou, Jiangsu, ChinaGeneral Surgery Department, Qinghai Provincial People’s Hospital, Xining, Qinghai, ChinaCenter for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd, Wuhan, ChinaGeneral Surgery Department, Qinghai Provincial People’s Hospital, Xining, Qinghai, ChinaGeneral Surgery Department, Qinghai Provincial People’s Hospital, Xining, Qinghai, ChinaGeneral Surgery Department, Qinghai Provincial People’s Hospital, Xining, Qinghai, ChinaGeneral Surgery Department, Qinghai Provincial People’s Hospital, Xining, Qinghai, ChinaGeneral Surgery Department, Qinghai Provincial People’s Hospital, Xining, Qinghai, ChinaCenter for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd, Wuhan, ChinaCenter for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd, Wuhan, ChinaGeneral Surgery Department, Qinghai Provincial People’s Hospital, Xining, Qinghai, ChinaIntroductionIn most instances, liver transplantation (LT) is the only available treatment for end‐stage liver diseases. However, LT could also induce serious liver diseases or injury, and the underlying mechanisms of LT-induced complications remain largely unknown, especially the mechanisms of the dysfunction of the immune system mediated by long noncoding RNAs (lncRNAs).MethodsIn this study, we globally analyzed the proportion of immune cells by using the transcriptome sequencing data (RNA-seq) of needle-core liver biopsies from pre- and post-transplantation recipients. Dysregulated lncRNAs were found to be correlated with the altered fractions of immune cells. We finally explored the potential targets of dysregulated lncRNAs and analyzed their functions in LT.ResultsWe found that in the samples, some immune cells changed significantly after LT, including CD4 T cells, NK cells and mast cells. The proportion of macrophages in different polarization states also changed significantly, with M0 macrophages increasing and M2 macrophages decreasing. Through weighted gene co-expression network analysis (WGCNA), 7 gene expression modules related to LT were identified. These modules were related to changes in the proportion of different immune cells. The functions of these modules represent the response modes of different functional genes after LT. Among these modules, MEtan and MEyellow modules were primarily enriched in apoptosis and inflammatory pathways. Twelve immunity-related lncRNAs were identified for the first time, and the regulatory network co-changing with immune cells was also identified. The co-expressed genes of these lncRNAs were highly enriched in apoptosis-related pathways. Many apoptosis-related genes were found to be up-regulated after LT.DiscussionIn summary, we speculated that the expression and regulation of these apoptotic genes may be related to the changes in the proportion of immune cells. Some of these lncRNAs and apoptosis-related genes have been reported to be related to cell proliferation and apoptosis. They are also potential biomarkers or therapeutic targets.https://www.frontiersin.org/articles/10.3389/fimmu.2023.1152742/fullliver transplantationlncRNAsimmune cellsco-expressionapoptosis |
| spellingShingle | Shile Wu Shile Wu Chao Cheng Wenjun Zhu Jinyu Yang Bei-bei He Song Li Xinsheng Wang Hao Guo Dong Chen Ya-min Guo Whole transcriptome analysis reveals that immune infiltration- lncRNAs are related to cellular apoptosis in liver transplantation Frontiers in Immunology liver transplantation lncRNAs immune cells co-expression apoptosis |
| title | Whole transcriptome analysis reveals that immune infiltration- lncRNAs are related to cellular apoptosis in liver transplantation |
| title_full | Whole transcriptome analysis reveals that immune infiltration- lncRNAs are related to cellular apoptosis in liver transplantation |
| title_fullStr | Whole transcriptome analysis reveals that immune infiltration- lncRNAs are related to cellular apoptosis in liver transplantation |
| title_full_unstemmed | Whole transcriptome analysis reveals that immune infiltration- lncRNAs are related to cellular apoptosis in liver transplantation |
| title_short | Whole transcriptome analysis reveals that immune infiltration- lncRNAs are related to cellular apoptosis in liver transplantation |
| title_sort | whole transcriptome analysis reveals that immune infiltration lncrnas are related to cellular apoptosis in liver transplantation |
| topic | liver transplantation lncRNAs immune cells co-expression apoptosis |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1152742/full |
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