RNA-Seq and Immune Repertoire Analysis of Normal and Hepatocellular Carcinoma Relapse After Liver Transplantation
Fansheng Guo,1 Xiaoye Yuan,2 Jinglin Cao,1 Xin Zhao,1 Yang Wang,1 Wenpeng Liu,1 Baowang Liu,1 Qiang Zeng1 1Department of Hepatobiliary Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China; 2Department of Gerontology, Hebei General Hospital, Shijia...
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| Format: | Article |
| Language: | English |
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Dove Medical Press
2023-09-01
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| Series: | International Journal of General Medicine |
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| Online Access: | https://www.dovepress.com/rna-seq-and-immune-repertoire-analysis-of-normal-and-hepatocellular-ca-peer-reviewed-fulltext-article-IJGM |
| _version_ | 1797672916097171456 |
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| author | Guo F Yuan X Cao J Zhao X Wang Y Liu W Liu B Zeng Q |
| author_facet | Guo F Yuan X Cao J Zhao X Wang Y Liu W Liu B Zeng Q |
| author_sort | Guo F |
| collection | DOAJ |
| description | Fansheng Guo,1 Xiaoye Yuan,2 Jinglin Cao,1 Xin Zhao,1 Yang Wang,1 Wenpeng Liu,1 Baowang Liu,1 Qiang Zeng1 1Department of Hepatobiliary Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China; 2Department of Gerontology, Hebei General Hospital, Shijiazhuang, 050000, People’s Republic of ChinaCorrespondence: Qiang Zeng, Department of Hepatobiliary Surgery, the Third Hospital of Hebei Medical University, No. 139, Ziqiang Road, Shijiazhuang, 050051, People’s Republic of China, Tel +86-15511308373, Email zengqiangtg@163.comBackground: Hepatocellular carcinoma (HCC) relapse is the main reason for the poor prognosis of HCC after Liver transplantation (LT). This study aimed to explore the molecular mechanisms and immune repertoire profiles of HCC relapse.Material and Methods: RNA-seq of blood samples from patients with normal (n=12) and HCC relapse (n=6) after LT was performed to identify differentially expressed genes (DEGs) and key signalling pathways. The DEGs and immune genes were further analyzed by bioinformatics. TRUST4 was used to analyze the differences in the immune repertoire between the two groups. Another 11 blood samples from patients with HCC who had received LT were collected for RT-qPCR verification of key genes.Results: A total of 131 upregulated and 157 downregulated genes were identified using RNA-seq, and GO enrichment analysis revealed that the top 15 pathways were immune-related. The PPI network identified 10 key genes. Immune infiltration analysis revealed a significant difference in the five immune cell types between the two groups. A total of 83 intersecting genes were obtained by intersecting DEGs and immune genes. 6 key genes, including MX1, ISG15, OAS1, PRF1, SPP1, and THBS1 were obtained according to the intersection of DEGs, PPI network top 10 genes and immune intersecting genes. Immune repertoire analysis showed that the usage frequency of variable (V) and joining (J) genes in the normal group was higher than that in the relapse group. RT-qPCR validation showed that the expression levels of key genes were consistent with the RNA-seq results.Conclusion: Our study identified key pathways and genes that could help determine whether transplant recipients are more prone to HCC relapse. Immune repertoire analysis revealed a difference in the usage frequency of VJ genes between the normal and relapse groups, providing a research direction for immunotherapy in patients with HCC relapse after liver transplantation.Keywords: liver transplantation, hepatocellular carcinoma relapse, RNA-sequencing, immune repertoire, variable and joining genes, V and J genes |
| first_indexed | 2024-03-11T21:38:09Z |
| format | Article |
| id | doaj.art-cf6b6a6ed62e4f039ca8df8f17687226 |
| institution | Directory Open Access Journal |
| issn | 1178-7074 |
| language | English |
| last_indexed | 2024-03-11T21:38:09Z |
| publishDate | 2023-09-01 |
| publisher | Dove Medical Press |
| record_format | Article |
| series | International Journal of General Medicine |
| spelling | doaj.art-cf6b6a6ed62e4f039ca8df8f176872262023-09-26T18:27:38ZengDove Medical PressInternational Journal of General Medicine1178-70742023-09-01Volume 164329434186916RNA-Seq and Immune Repertoire Analysis of Normal and Hepatocellular Carcinoma Relapse After Liver TransplantationGuo FYuan XCao JZhao XWang YLiu WLiu BZeng QFansheng Guo,1 Xiaoye Yuan,2 Jinglin Cao,1 Xin Zhao,1 Yang Wang,1 Wenpeng Liu,1 Baowang Liu,1 Qiang Zeng1 1Department of Hepatobiliary Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China; 2Department of Gerontology, Hebei General Hospital, Shijiazhuang, 050000, People’s Republic of ChinaCorrespondence: Qiang Zeng, Department of Hepatobiliary Surgery, the Third Hospital of Hebei Medical University, No. 139, Ziqiang Road, Shijiazhuang, 050051, People’s Republic of China, Tel +86-15511308373, Email zengqiangtg@163.comBackground: Hepatocellular carcinoma (HCC) relapse is the main reason for the poor prognosis of HCC after Liver transplantation (LT). This study aimed to explore the molecular mechanisms and immune repertoire profiles of HCC relapse.Material and Methods: RNA-seq of blood samples from patients with normal (n=12) and HCC relapse (n=6) after LT was performed to identify differentially expressed genes (DEGs) and key signalling pathways. The DEGs and immune genes were further analyzed by bioinformatics. TRUST4 was used to analyze the differences in the immune repertoire between the two groups. Another 11 blood samples from patients with HCC who had received LT were collected for RT-qPCR verification of key genes.Results: A total of 131 upregulated and 157 downregulated genes were identified using RNA-seq, and GO enrichment analysis revealed that the top 15 pathways were immune-related. The PPI network identified 10 key genes. Immune infiltration analysis revealed a significant difference in the five immune cell types between the two groups. A total of 83 intersecting genes were obtained by intersecting DEGs and immune genes. 6 key genes, including MX1, ISG15, OAS1, PRF1, SPP1, and THBS1 were obtained according to the intersection of DEGs, PPI network top 10 genes and immune intersecting genes. Immune repertoire analysis showed that the usage frequency of variable (V) and joining (J) genes in the normal group was higher than that in the relapse group. RT-qPCR validation showed that the expression levels of key genes were consistent with the RNA-seq results.Conclusion: Our study identified key pathways and genes that could help determine whether transplant recipients are more prone to HCC relapse. Immune repertoire analysis revealed a difference in the usage frequency of VJ genes between the normal and relapse groups, providing a research direction for immunotherapy in patients with HCC relapse after liver transplantation.Keywords: liver transplantation, hepatocellular carcinoma relapse, RNA-sequencing, immune repertoire, variable and joining genes, V and J geneshttps://www.dovepress.com/rna-seq-and-immune-repertoire-analysis-of-normal-and-hepatocellular-ca-peer-reviewed-fulltext-article-IJGMliver transplantationhepatocellular carcinoma relapserna-sequencingimmune repertoirevariable and joining genesv and j genes |
| spellingShingle | Guo F Yuan X Cao J Zhao X Wang Y Liu W Liu B Zeng Q RNA-Seq and Immune Repertoire Analysis of Normal and Hepatocellular Carcinoma Relapse After Liver Transplantation International Journal of General Medicine liver transplantation hepatocellular carcinoma relapse rna-sequencing immune repertoire variable and joining genes v and j genes |
| title | RNA-Seq and Immune Repertoire Analysis of Normal and Hepatocellular Carcinoma Relapse After Liver Transplantation |
| title_full | RNA-Seq and Immune Repertoire Analysis of Normal and Hepatocellular Carcinoma Relapse After Liver Transplantation |
| title_fullStr | RNA-Seq and Immune Repertoire Analysis of Normal and Hepatocellular Carcinoma Relapse After Liver Transplantation |
| title_full_unstemmed | RNA-Seq and Immune Repertoire Analysis of Normal and Hepatocellular Carcinoma Relapse After Liver Transplantation |
| title_short | RNA-Seq and Immune Repertoire Analysis of Normal and Hepatocellular Carcinoma Relapse After Liver Transplantation |
| title_sort | rna seq and immune repertoire analysis of normal and hepatocellular carcinoma relapse after liver transplantation |
| topic | liver transplantation hepatocellular carcinoma relapse rna-sequencing immune repertoire variable and joining genes v and j genes |
| url | https://www.dovepress.com/rna-seq-and-immune-repertoire-analysis-of-normal-and-hepatocellular-ca-peer-reviewed-fulltext-article-IJGM |
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