Immune Classification and Immune Landscape Analysis of Triple-Negative Breast Cancer
Background: To classify triple-negative breast cancer (TNBC) immunotyping using the public database, analyze the differences between subtypes in terms of clinical characteristics and explore the role and clinical significance of immune subtypes in TNBC immunotherapy.Methods: We downloaded TNBC data...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-11-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.710534/full |
| _version_ | 1819045859701030912 |
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| author | Shaojun Hu Xiusheng Qu Yu Jiao Jiahui Hu Bo Wang |
| author_facet | Shaojun Hu Xiusheng Qu Yu Jiao Jiahui Hu Bo Wang |
| author_sort | Shaojun Hu |
| collection | DOAJ |
| description | Background: To classify triple-negative breast cancer (TNBC) immunotyping using the public database, analyze the differences between subtypes in terms of clinical characteristics and explore the role and clinical significance of immune subtypes in TNBC immunotherapy.Methods: We downloaded TNBC data from the cBioPortal and GEO databases. The immune genes were grouped to obtain immune gene modules and annotate their biological functions. Log-rank tests and Cox regression were used to evaluate the prognosis of immune subtypes (IS). Drug sensitivity analysis was also performed for the differences among immune subtypes in immunotherapy and chemotherapy. In addition, dimension reduction analysis based on graph learning was utilized to reveal the internal structure of the immune system and visualize the distribution of patients.Results: Significant differences in prognosis were observed between subtypes (IS1, IS2, and IS3), with the best in IS3 and the worst in IS1. The sensitivity of IS3 to immunotherapy and chemotherapy was better than the other two subtypes. In addition, Immune landscape analysis found the intra-class heterogeneity of immune subtypes and further classified IS3 subtypes (IS3A and IS3B). Immune-related genes were divided into seven functional modules (The turquoise module has the worst prognosis). Five hub genes (RASSF5, CD8A, ICOS, IRF8, and CD247) were screened out as the final characteristic genes related to poor prognosis by low expression.Conclusions: The immune subtypes of TNBC were significantly different in prognosis, gene mutation, immune infiltration, drug sensitivity, and heterogeneity. We validated the independent role of immune subtypes in tumor progression and immunotherapy for TNBC. This study provides a new perspective for personalized immunotherapy and the prognosis evaluation of TNBC patients in the future. |
| first_indexed | 2024-12-21T10:35:16Z |
| format | Article |
| id | doaj.art-b2ddc5b1b8764c1fb275fe9bb8bd2618 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-21T10:35:16Z |
| publishDate | 2021-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-b2ddc5b1b8764c1fb275fe9bb8bd26182022-12-21T19:07:05ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-11-011210.3389/fgene.2021.710534710534Immune Classification and Immune Landscape Analysis of Triple-Negative Breast CancerShaojun Hu0Xiusheng Qu1Yu Jiao2Jiahui Hu3Bo Wang4Oncology Department, First Affiliated Hospital of Jiamusi University, Jiamusi, ChinaChemotherapy Department, First Affiliated Hospital of Jiamusi University, Jiamusi, ChinaOncology Department, First Affiliated Hospital of Jiamusi University, Jiamusi, ChinaChemotherapy Department, First Affiliated Hospital of Jiamusi University, Jiamusi, ChinaOncology Department, First Affiliated Hospital of Jiamusi University, Jiamusi, ChinaBackground: To classify triple-negative breast cancer (TNBC) immunotyping using the public database, analyze the differences between subtypes in terms of clinical characteristics and explore the role and clinical significance of immune subtypes in TNBC immunotherapy.Methods: We downloaded TNBC data from the cBioPortal and GEO databases. The immune genes were grouped to obtain immune gene modules and annotate their biological functions. Log-rank tests and Cox regression were used to evaluate the prognosis of immune subtypes (IS). Drug sensitivity analysis was also performed for the differences among immune subtypes in immunotherapy and chemotherapy. In addition, dimension reduction analysis based on graph learning was utilized to reveal the internal structure of the immune system and visualize the distribution of patients.Results: Significant differences in prognosis were observed between subtypes (IS1, IS2, and IS3), with the best in IS3 and the worst in IS1. The sensitivity of IS3 to immunotherapy and chemotherapy was better than the other two subtypes. In addition, Immune landscape analysis found the intra-class heterogeneity of immune subtypes and further classified IS3 subtypes (IS3A and IS3B). Immune-related genes were divided into seven functional modules (The turquoise module has the worst prognosis). Five hub genes (RASSF5, CD8A, ICOS, IRF8, and CD247) were screened out as the final characteristic genes related to poor prognosis by low expression.Conclusions: The immune subtypes of TNBC were significantly different in prognosis, gene mutation, immune infiltration, drug sensitivity, and heterogeneity. We validated the independent role of immune subtypes in tumor progression and immunotherapy for TNBC. This study provides a new perspective for personalized immunotherapy and the prognosis evaluation of TNBC patients in the future.https://www.frontiersin.org/articles/10.3389/fgene.2021.710534/fulltriple-negative breast cancerTCGA databaseimmune microenvironmentimmune subtypeimmunotherapy |
| spellingShingle | Shaojun Hu Xiusheng Qu Yu Jiao Jiahui Hu Bo Wang Immune Classification and Immune Landscape Analysis of Triple-Negative Breast Cancer Frontiers in Genetics triple-negative breast cancer TCGA database immune microenvironment immune subtype immunotherapy |
| title | Immune Classification and Immune Landscape Analysis of Triple-Negative Breast Cancer |
| title_full | Immune Classification and Immune Landscape Analysis of Triple-Negative Breast Cancer |
| title_fullStr | Immune Classification and Immune Landscape Analysis of Triple-Negative Breast Cancer |
| title_full_unstemmed | Immune Classification and Immune Landscape Analysis of Triple-Negative Breast Cancer |
| title_short | Immune Classification and Immune Landscape Analysis of Triple-Negative Breast Cancer |
| title_sort | immune classification and immune landscape analysis of triple negative breast cancer |
| topic | triple-negative breast cancer TCGA database immune microenvironment immune subtype immunotherapy |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.710534/full |
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