Identification of Immune Microenvironment Changes and the Expression of Immune-Related Genes in Liver Cirrhosis
Liver inflammation and the immune response have been recognized as critical contributors to cirrhosis pathogenesis. Immunity-related genes (IRGs) play an essential role in immune cell infiltration and immune reactions; however, the changes in the immune microenvironment and the expression of IRGs in...
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| Format: | Article |
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Frontiers Media S.A.
2022-07-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2022.918445/full |
| _version_ | 1811225904898113536 |
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| author | Yuwei Liu Yuwei Liu Yuwei Liu Yutong Dong Yutong Dong Yutong Dong Xiaojing Wu Xiaojing Wu Xiaojing Wu Xiaomei Wang Xiaomei Wang Xiaomei Wang Junqi Niu Junqi Niu Junqi Niu |
| author_facet | Yuwei Liu Yuwei Liu Yuwei Liu Yutong Dong Yutong Dong Yutong Dong Xiaojing Wu Xiaojing Wu Xiaojing Wu Xiaomei Wang Xiaomei Wang Xiaomei Wang Junqi Niu Junqi Niu Junqi Niu |
| author_sort | Yuwei Liu |
| collection | DOAJ |
| description | Liver inflammation and the immune response have been recognized as critical contributors to cirrhosis pathogenesis. Immunity-related genes (IRGs) play an essential role in immune cell infiltration and immune reactions; however, the changes in the immune microenvironment and the expression of IRGs involved in cirrhosis remain unclear. CD45+ liver cell single-cell RNA (scRNA) sequencing data (GSE136103) from patients with cirrhosis were analyzed. The clusters were identified as known cell types through marker genes according to previous studies. GO and KEGG analyses among differentially expressed genes (DEGs) were performed. DEGs were screened to identify IRGs based on the ImmPort database. The protein-protein interaction (PPI) network of IRGs was generated using the STRING database. IRGs activity was calculated using the AUCell package. RNA microarray expression data (GSE45050) of cirrhosis were analyzed to confirm common IRGs and IRGs activity. Relevant regulatory transcription factors (TFs) were identified from the Human TFDB database. A total of ten clusters were obtained. CD8+ T cells and NK cells were significantly decreased in patients with cirrhosis, while CD4+ T memory cells were increased. Enrichment analyses showed that the DEGs focused on the regulation of immune cell activation and differentiation, NK-cell mediated cytotoxicity, and antigen processing and presentation. Four common TFs, IRF8, NR4A2, IKZF3, and REL were expressed in both the NK cluster and the DEGs of liver tissues. In conclusion, we proposed that the reduction of the CD8+ T cell cluster and NK cells, as well as the infiltration of CD4+ memory T cells, contributed to immune microenvironment changes in cirrhosis. IRF8, NR4A2, IKZF3, and REL may be involved in the transcriptional regulation of NK cells in liver fibrosis. The identified DEGs, IRGs, and pathways may serve critical roles in the development and progression of liver fibrosis. |
| first_indexed | 2024-04-12T09:15:11Z |
| format | Article |
| id | doaj.art-ac1c9ced020948d9905f52964bb1e886 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-12T09:15:11Z |
| publishDate | 2022-07-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Immunology |
| spelling | doaj.art-ac1c9ced020948d9905f52964bb1e8862022-12-22T03:38:51ZengFrontiers Media S.A.Frontiers in Immunology1664-32242022-07-011310.3389/fimmu.2022.918445918445Identification of Immune Microenvironment Changes and the Expression of Immune-Related Genes in Liver CirrhosisYuwei Liu0Yuwei Liu1Yuwei Liu2Yutong Dong3Yutong Dong4Yutong Dong5Xiaojing Wu6Xiaojing Wu7Xiaojing Wu8Xiaomei Wang9Xiaomei Wang10Xiaomei Wang11Junqi Niu12Junqi Niu13Junqi Niu14Department of Hepatology, Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, ChinaKey Laboratory of Zoonosis Research, Ministry of Education, The First Hospital of Jilin University, Changchun, ChinaKey Laboratory of Organ Transplantation, Ministry of Education, The First Hospital of Jilin University, Changchun, ChinaDepartment of Hepatology, Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, ChinaKey Laboratory of Zoonosis Research, Ministry of Education, The First Hospital of Jilin University, Changchun, ChinaKey Laboratory of Organ Transplantation, Ministry of Education, The First Hospital of Jilin University, Changchun, ChinaDepartment of Hepatology, Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, ChinaKey Laboratory of Zoonosis Research, Ministry of Education, The First Hospital of Jilin University, Changchun, ChinaKey Laboratory of Organ Transplantation, Ministry of Education, The First Hospital of Jilin University, Changchun, ChinaDepartment of Hepatology, Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, ChinaKey Laboratory of Zoonosis Research, Ministry of Education, The First Hospital of Jilin University, Changchun, ChinaKey Laboratory of Organ Transplantation, Ministry of Education, The First Hospital of Jilin University, Changchun, ChinaDepartment of Hepatology, Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, ChinaKey Laboratory of Zoonosis Research, Ministry of Education, The First Hospital of Jilin University, Changchun, ChinaKey Laboratory of Organ Transplantation, Ministry of Education, The First Hospital of Jilin University, Changchun, ChinaLiver inflammation and the immune response have been recognized as critical contributors to cirrhosis pathogenesis. Immunity-related genes (IRGs) play an essential role in immune cell infiltration and immune reactions; however, the changes in the immune microenvironment and the expression of IRGs involved in cirrhosis remain unclear. CD45+ liver cell single-cell RNA (scRNA) sequencing data (GSE136103) from patients with cirrhosis were analyzed. The clusters were identified as known cell types through marker genes according to previous studies. GO and KEGG analyses among differentially expressed genes (DEGs) were performed. DEGs were screened to identify IRGs based on the ImmPort database. The protein-protein interaction (PPI) network of IRGs was generated using the STRING database. IRGs activity was calculated using the AUCell package. RNA microarray expression data (GSE45050) of cirrhosis were analyzed to confirm common IRGs and IRGs activity. Relevant regulatory transcription factors (TFs) were identified from the Human TFDB database. A total of ten clusters were obtained. CD8+ T cells and NK cells were significantly decreased in patients with cirrhosis, while CD4+ T memory cells were increased. Enrichment analyses showed that the DEGs focused on the regulation of immune cell activation and differentiation, NK-cell mediated cytotoxicity, and antigen processing and presentation. Four common TFs, IRF8, NR4A2, IKZF3, and REL were expressed in both the NK cluster and the DEGs of liver tissues. In conclusion, we proposed that the reduction of the CD8+ T cell cluster and NK cells, as well as the infiltration of CD4+ memory T cells, contributed to immune microenvironment changes in cirrhosis. IRF8, NR4A2, IKZF3, and REL may be involved in the transcriptional regulation of NK cells in liver fibrosis. The identified DEGs, IRGs, and pathways may serve critical roles in the development and progression of liver fibrosis.https://www.frontiersin.org/articles/10.3389/fimmu.2022.918445/fullcirrhosissingle-cell RNA sequencingimmunity-related genesdifferentially expressed genesimmune microenvironment |
| spellingShingle | Yuwei Liu Yuwei Liu Yuwei Liu Yutong Dong Yutong Dong Yutong Dong Xiaojing Wu Xiaojing Wu Xiaojing Wu Xiaomei Wang Xiaomei Wang Xiaomei Wang Junqi Niu Junqi Niu Junqi Niu Identification of Immune Microenvironment Changes and the Expression of Immune-Related Genes in Liver Cirrhosis Frontiers in Immunology cirrhosis single-cell RNA sequencing immunity-related genes differentially expressed genes immune microenvironment |
| title | Identification of Immune Microenvironment Changes and the Expression of Immune-Related Genes in Liver Cirrhosis |
| title_full | Identification of Immune Microenvironment Changes and the Expression of Immune-Related Genes in Liver Cirrhosis |
| title_fullStr | Identification of Immune Microenvironment Changes and the Expression of Immune-Related Genes in Liver Cirrhosis |
| title_full_unstemmed | Identification of Immune Microenvironment Changes and the Expression of Immune-Related Genes in Liver Cirrhosis |
| title_short | Identification of Immune Microenvironment Changes and the Expression of Immune-Related Genes in Liver Cirrhosis |
| title_sort | identification of immune microenvironment changes and the expression of immune related genes in liver cirrhosis |
| topic | cirrhosis single-cell RNA sequencing immunity-related genes differentially expressed genes immune microenvironment |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2022.918445/full |
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