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Gene expression patterns associated with tumor-infiltrating CD4+ and CD8+ T cells in invasive breast carcinomas
Zhanwei Wang1, Xi Yang2, Junjun Shen2
1Department of Breast Surgery, Huzhou Central Hospital, Affiliated Central Hospital HuZhou University, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, Zhejiang Province 313000, China.
Background:
Breast carcinoma is one of the most common tumors in women. The immune microenvironment, especially T cell infiltration, is related to the occurrence and prognosis of breast carcinoma.
Objective:
This study investigated the gene expression patterns associated with tumor-infiltrating CD4+ and CD8+ T cells in invasive breast carcinomas.
Methods:
The gene expression data and corresponding clinical phenotype data from the Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) were downloaded. The stromal and immune score were calculated using ESTIMATE. The differentially expressed genes (DEGs) with a high vs. low stromal score and a high vs. low immune score were screened and then functionally enriched. The tumor-infiltrating immune cells were investigated using the Cibersort algorithm, and the CD4+ and CD8+ T cell-related genes were identified using a Spearman correlation test of infiltrating abundance with the DEGs. Moreover, the miRNA-mRNA pairs and lncRNA-miRNA pairs were predicted to construct the competing endogenous RNAs (ceRNA) network. Kaplan-Meier (K-M) survival curves were also plotted.
Results:
In total, 478 DEGs with a high vs. low stromal score and 796 DEGs with a high vs. low immune score were identified. In addition, 39 CD4+ T cell-related genes and 78 CD8+ T cell-related genes were identified; of these, 14 genes were significantly associated with the prognosis of BRCA patients. Moreover, for CD4+ T cell-related genes, the chr22-38_28785274-29006793.1-miR-34a/c-5p-CAPN6 axis was identified from the ceRNA network, whereas the chr22-38_28785274-29006793.1-miR-494-3p-SLC9A7 axis was identified for CD8+ T cell-related genes.
Conclusions:
The chr22-38_28785274-29006793.1-miR-34a/c-5p-CAPN6 axis and the chr22-38_28785274-29006793.1-miR-494-3p-SLC9A7 axis might regulate cellular activities associated with CD4+ and CD8+ T cell infiltration, respectively, in BRCA.
