In this study, the RNA-seq data and clinical phenotype data from TCGA-BRCA were used to investigate the gene expression pattern in the immune response in BRCA progression. A total of 478 DEGs with a high vs. low stromal score, and 796 DEGs with a high vs. low immune score were identified, and the overlapping DEGs were found to be implicated in ion transmembrane transport, regulation of pH, and extrinsic apoptotic signaling pathways. In addition, a total of 39 CD4 + T cell-related genes and 78 CD8 + T cell-related genes were identified, of which 14 genes were related to prognosis of BRCA patients, for example, MUC2. Moreover, for CD4 + T cell-related genes, the chr22-38_28785274-29006793.1–miR-34a/c-5p–CAPN6 axis was identified in the ceRNA network and for CD8 + T cell-related genes, the chr22-38_28785274-29006793.1–miR-494-3p–SLC9A7 axis was identified.
MUC2, also termed mucin-2, belongs to the mucin protein family, which are high molecular weight glycoproteins secreted to form an insoluble mucous barrier that protects the gut lumen [33]. MUC2 was found to be expressed in breast mucinous carcinomas, and Matsukita et al. indicated that overexpression of MUC2 in mucinous carcinoma might serve as a barrier to attenuate tumor aggressiveness [34]. Astashchanka et al. showed that MUC2 participates in the regulation of proliferation, apoptosis, and metastasis of breast carcinoma cells, indicating roles of MUC2 in therapy and in clinical outcome prediction in breast carcinoma [35]. In our study, the expression of MUC2 was correlated with both CD4 + and CD8 + T cell infiltration and was associated with prognosis of BRCA patients. Therefore, we speculated that MUC2 might regulate the aggressiveness of BRCA; this process is probably accompanied by T cell infiltration.
For CD4 + T cell-related genes, the chr22-38_28785274-29006793.1–miR-34a/c-5p–CAPN6 axis was identified from the ceRNA network. The miR-34 family (miR-34a/b/c) is composed of tumor suppressors, functioning in inhibiting proliferation, migration and inducing apoptosis, and are also important mediators of the p53 signaling pathway [36, 37]. It has been reported that miR-34a serves as a tumor suppressor in triple-negative breast carcinomas by targeting the proto-oncogene c-SRC [38]. Similarly, Xiao et al. found that miR-34a can inhibit glycolysis and proliferation of breast carcinoma cells in breast carcinomas by directly targeting lactate dehydrogenase A, whose overexpression is associated with tumor growth and metastasis [39]. CAPN6, also termed calpain-6, is a member of an intracellular cysteine protease family, and this family is found to be abnormally expressed in malignant tumors [40]. Calpains are reported to be involved in various cellular activities in breast carcinomas, including cellular survival, apoptosis and migration [41]. MacLeod et al. suggested that calpain 1 and 2 play a pro-tumorigenic role in HER2 + breast cancer, whereas tumorigenesis can be delayed by disrupting calpain 1 and 2 expression [42]. Calpain 6 has been reported to relate to tumorigenesis and unfavorable prognosis in head and neck squamous cell carcinoma [40], and is considered to be a possible target in the treatment of sarcomas [43]. The role of calpain 6 in breast carcinomas was rarely reported. A previous study showed that calpain 1 and miR-34a/c were associated with kanamycin-induced inner ear cell apoptosis [44]. In our study, CAPN6/calpain 6 was predicted to be a target of miR-34a/c-5p, which was regulated by the lncRNA chr22-38_28785274-29006793.1. The role of the lncRNA chr22-38_28785274-29006793.1 has not yet been reported. We speculated that the chr22-38_28785274-29006793.1–miR-34a/c-5p–CAPN6 axis might regulate cellular activities associated with CD4 + T cell infiltration in BRCA.
The abnormal expression of miR-494 has been reported in various cancers. However, the role of miR-494 in carcinogenesis is contradictory, including a tumor suppressor role [45, 46] and an oncogenic role [47, 48]. Zhan et al. revealed that miR-494 can inhibit the progression and metastasis of breast carcinomas by targeting P21 (RAC1) activated kinase 1 [49]. The proliferation and migration of MDA‑MB‑231 and MDA‑MB‑468 breast carcinoma cells can be promoted by highly expressing miR‑183 or miR‑494 [50]. SLC9A7, also termed NHE7, is a (Na+, K+)/H + exchanger, functioning in regulating cellular pH and ion homeostasis [51]. pH has a crucial role in regulating cell motility and metastasis. The metastatic potential of breast carcinoma cells can be enhanced by exposure to alkaline pH [52]. Onishi et al. found that SLC9A7/NHE7 can promote adhesion, invasion, and oncogenesis of MDA-MB-231 breast carcinoma cells [53]. In our study, the chr22-38_28785274-29006793.1–miR-494-3p–SLC9A7 axis was identified from the CD8 + T cell-related ceRNA network. Hence, we suggested that the chr22-38_28785274-29006793.1–miR-494-3p–SLC9A7 axis might regulate cellular activities associated with CD8 + T cell infiltration in BRCA.
Although several novel findings were found in this study, there were some limitations. (1) Our study preliminarily analyzed the gene expression pattern of tumor-infiltrating CD4 + and CD8 + T cells of BRCA. However, further experiments are needed to confirm the expression of the DEGs and the predicted ceRNA axes. (2) The correlations between prognosis and the 14 identified genes should be further investigated using clinical trials. (3) The predicted chemical–gene interactions should be confirmed to provide research topics for the treatment of BRCA.