Pan-cancer illumination of TRIM gene family reveals immunology regulation and potential therapeutic implications
Abstract Background The tripartite motif (TRIM) proteins function as important regulators in innate immunity, tumorigenesis, cell differentiation and ontogenetic development. However, we still lack knowledge about the genetic and transcriptome alterations landscape of TRIM proteins across cancer typ...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-12-01
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| Series: | Human Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s40246-022-00441-9 |
| _version_ | 1811315381764096000 |
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| author | Yueying Gao Tao Pan Gang Xu Si Li Jing Guo Ya Zhang Qi Xu Jiwei Pan Yanlin Ma Juan Xu Yongsheng Li |
| author_facet | Yueying Gao Tao Pan Gang Xu Si Li Jing Guo Ya Zhang Qi Xu Jiwei Pan Yanlin Ma Juan Xu Yongsheng Li |
| author_sort | Yueying Gao |
| collection | DOAJ |
| description | Abstract Background The tripartite motif (TRIM) proteins function as important regulators in innate immunity, tumorigenesis, cell differentiation and ontogenetic development. However, we still lack knowledge about the genetic and transcriptome alterations landscape of TRIM proteins across cancer types. Methods We comprehensively reviewed and characterized the perturbations of TRIM genes across > 10,000 samples across 33 cancer types. Genetic mutations and transcriptome of TRIM genes were analyzed by diverse computational methods. A TRIMs score index was calculated based on the expression of TRIM genes. The correlation between TRIMs scores and clinical associations, immune cell infiltrations and immunotherapy response were analyzed by correlation coefficients and gene set enrichment analysis. Results Alterations in TRIM genes and protein levels frequently emerge in a wide range of tumors and affect expression of TRIM genes. In particular, mutations located in domains are likely to be deleterious mutations. Perturbations of TRIM genes are correlated with expressions of immune checkpoints and immune cell infiltrations, which further regulated the cancer- and immune-related pathways. Moreover, we proposed a TRIMs score index, which can accurately predict the clinical outcome of cancer patients. TRIMs scores of patients are correlated with clinical survival and immune therapy response across cancer types. Identifying the TRIM genes with genetic and transcriptome alterations will directly contribute to cancer therapy in the context of predictive, preventive, and personalized medicine. Conclusions Our study provided a comprehensive analysis and resource for guiding both mechanistic and therapeutic analyses of the roles of TRIM genes in cancer. |
| first_indexed | 2024-04-13T11:29:20Z |
| format | Article |
| id | doaj.art-1321c9b7eb4d41e1b2c07ce585f09005 |
| institution | Directory Open Access Journal |
| issn | 1479-7364 |
| language | English |
| last_indexed | 2024-04-13T11:29:20Z |
| publishDate | 2022-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Human Genomics |
| spelling | doaj.art-1321c9b7eb4d41e1b2c07ce585f090052022-12-22T02:48:36ZengBMCHuman Genomics1479-73642022-12-0116111510.1186/s40246-022-00441-9Pan-cancer illumination of TRIM gene family reveals immunology regulation and potential therapeutic implicationsYueying Gao0Tao Pan1Gang Xu2Si Li3Jing Guo4Ya Zhang5Qi Xu6Jiwei Pan7Yanlin Ma8Juan Xu9Yongsheng Li10Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical UniversityHainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical UniversityCollege of Biomedical Information and Engineering, Hainan Medical UniversityCollege of Biomedical Information and Engineering, Hainan Medical UniversityCollege of Biomedical Information and Engineering, Hainan Medical UniversityCollege of Biomedical Information and Engineering, Hainan Medical UniversityCollege of Biomedical Information and Engineering, Hainan Medical UniversityCollege of Biomedical Information and Engineering, Hainan Medical UniversityHainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical UniversityCollege of Bioinformatics Science and Technology, Harbin Medical UniversityHainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical UniversityAbstract Background The tripartite motif (TRIM) proteins function as important regulators in innate immunity, tumorigenesis, cell differentiation and ontogenetic development. However, we still lack knowledge about the genetic and transcriptome alterations landscape of TRIM proteins across cancer types. Methods We comprehensively reviewed and characterized the perturbations of TRIM genes across > 10,000 samples across 33 cancer types. Genetic mutations and transcriptome of TRIM genes were analyzed by diverse computational methods. A TRIMs score index was calculated based on the expression of TRIM genes. The correlation between TRIMs scores and clinical associations, immune cell infiltrations and immunotherapy response were analyzed by correlation coefficients and gene set enrichment analysis. Results Alterations in TRIM genes and protein levels frequently emerge in a wide range of tumors and affect expression of TRIM genes. In particular, mutations located in domains are likely to be deleterious mutations. Perturbations of TRIM genes are correlated with expressions of immune checkpoints and immune cell infiltrations, which further regulated the cancer- and immune-related pathways. Moreover, we proposed a TRIMs score index, which can accurately predict the clinical outcome of cancer patients. TRIMs scores of patients are correlated with clinical survival and immune therapy response across cancer types. Identifying the TRIM genes with genetic and transcriptome alterations will directly contribute to cancer therapy in the context of predictive, preventive, and personalized medicine. Conclusions Our study provided a comprehensive analysis and resource for guiding both mechanistic and therapeutic analyses of the roles of TRIM genes in cancer.https://doi.org/10.1186/s40246-022-00441-9TRIM genesPan-cancerImmune pathwaysImmunotherapy response |
| spellingShingle | Yueying Gao Tao Pan Gang Xu Si Li Jing Guo Ya Zhang Qi Xu Jiwei Pan Yanlin Ma Juan Xu Yongsheng Li Pan-cancer illumination of TRIM gene family reveals immunology regulation and potential therapeutic implications Human Genomics TRIM genes Pan-cancer Immune pathways Immunotherapy response |
| title | Pan-cancer illumination of TRIM gene family reveals immunology regulation and potential therapeutic implications |
| title_full | Pan-cancer illumination of TRIM gene family reveals immunology regulation and potential therapeutic implications |
| title_fullStr | Pan-cancer illumination of TRIM gene family reveals immunology regulation and potential therapeutic implications |
| title_full_unstemmed | Pan-cancer illumination of TRIM gene family reveals immunology regulation and potential therapeutic implications |
| title_short | Pan-cancer illumination of TRIM gene family reveals immunology regulation and potential therapeutic implications |
| title_sort | pan cancer illumination of trim gene family reveals immunology regulation and potential therapeutic implications |
| topic | TRIM genes Pan-cancer Immune pathways Immunotherapy response |
| url | https://doi.org/10.1186/s40246-022-00441-9 |
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