In this paper, the DEGs between normal breast tissue and TNBC tissue were obtained from 4 chips. The GO analysis indicated that the identified DEGs were related to mitotic nuclear division, cell division, sister chromatid cohesion, positive regulation of cell proliferation, cell chemotaxis, cell proliferation, heparin binding, chemokine activity, integrin binding, protein homodimerization activity, protein binding and metalloendopeptidase activity. The KEGG analysis indicated that the DEGs were related to ECM-receptor interaction, oocyte meiosis, cell cycle, focal adhesion, pathways in cancer and cytokine-cytokinereceptor interaction. This is consistent with the active proliferation of TNBC cells.
The PPI network shows the relationship between the proteins expressed by these genes. Due to the large number of proteins in the PPI network and the complex network relationship, it was necessary to further explore the more important gene modules through module analysis. PPI network analysis and module analysis of DEGs finally obtained 47 genes in 4 clusters. Survival analysis is an important method of studying tumour-associated genes. Due to the limitation of clinical follow-up data sources, RFS was used as the observation index of survival analysis, and MFS was used for verification in this paper. Through the survival analysis, 14 genes closely related to the prognosis of TNBC were obtained, namely, CCNB1, AURKB, KIF20A, BUB1B, DLGAP5, CXCL11, CXCL9, CXCL10, CXCL12, IGF1, FN1, CFD, SGO2 and CDCA5.
The cell cycle consists of five phases: G0 (gap 0), G1, S (synthesis), G2, and M (mitosis). Mitosis proceeds in five phases: prophase, prometaphase, metaphase, anaphase, and telophase [10].To ensure that only healthy cells proliferate, checkpoints have evolved that induce cell-cycle arrest in response to the detection of defects that may have arisen during DNA replication or other steps leading to mitosis [11]. The abnormal distribution of cells throughout the cell cycle is a hallmark of human cancer due to accumulating alterations of genes in the cell cycle pathway, possibly resulting in impaired abilities of cell division, cell proliferation and DNA damage response [12].
Among the high-risk genes found in this paper, the genes related to cell cycle and mitosis included AURKB, BUB1B, SGO2, CDCA5, CCNB1, DLGAP5 and KIF20A. These genes were overexpressed in TNBC and were associated with poor prognosis. AURKB is a member of the serine/threonine kinase family and is a major member of the chromosome passenger complex [13], which plays a key role in chromatin condensation and segregation and cytokinesis. Genetic instability caused by overexpression of AURKB is a direct cause of tumour formation [14]. Previous studies have found that AURKB expression is upregulated in leukemia, lymphoma, liver cancer and breast cancer and is associated with poor prognosis, which is consistent with the results of this study [15–18]. BUB1B encodes a kinase involved in the spindle assembly checkpoint and chromosome separation [19]. During the G2 phase, BUB1B inhibits anaphase-promoting complex/cyclosome activity, allowing cyclin B to accumulate before mitosis begins and slows the cell cycle [20]. Previous studies have found that BUB1B expression is upregulated in prostate cancer, breast cancer and lung cancer and is associated with poor prognosis [21–23]. SGO2 is a centromere-localized protein whose main function is to protect the cohesin of the sister chromatid from degradation. SGO2 regulates the localization of chromosomal passenger proteins [24] and mediates spindle assembly and chromosome congression to prevent the generation of chromosomal instability associated with malignant cell transformation [25]. SGO2 is also a key substrate of AURKB, which plays a central role in ensuring faithful chromosome segregation [26]. CDCA5 is a substrate of the anaphase-promoting complex and participates in the regulation of sister chromatid cohesion [27]. Previous studies have found that CDCA5 expression is upregulated in lung cancer and hepatocellular carcinoma and is associated with poor prognosis [28, 29]. CCNB1 belongs to a highly conserved family of cyclins that regulates the cell cycle and promotes cell proliferation. It is essential to control the cell cycle during G2/M transformation. Previous studies have found that CCNB1 overexpressed in ER-positive breast cancer and is associated with poor prognosis [30]. DLGAP5 belongs to the discs large-associated protein family, encodes the disc large homolog 7 (DLG7) protein, and controls on spindle stability [31, 32]. The overexpression of DLGAP5 in colorectal cancer and prostate cancer is associated with poor prognosis [33, 34]. KIF20A is a member of the kinesin super family − 6 that participates in spindle assembly and interacts with mitotic regulators [35]. The overexpression of KIF20A in hepatocellular carcinoma and lung adenocarcinoma is associated with poor prognosis [36, 37].
CXCL9, CXCL10, CXCL11, and CXCL12 belong to the chemokine family. They are small molecular cytokines that are produced by many kinds of cells. After binding with the receptor, they mediate cell migration, activate antigen-presenting cells and immune active cells, and regulate the immune process of the body. In this study, we found that CXCL9-11 was overexpressed in TNBC, CXCL12 was not overexpressed, and patients with overexpressed CXCL9-12 had a better prognosis. Possible reasons were that the large amount of CXCL9-12 can promote the infiltration of cytotoxic T lymphocytes into the tumour cell area to kill tumour cells and induce T or NK cells to inhibit tumour angiogenesis [38–43].
IGF1 is a key growth factor of the mammary terminal end bud and for ductal formation during development, and it also plays an important role in breast cancer development, progression and metastasis [44, 45]. Upregulating IGF1 may promote TNBC progression [46]. However, in this study, IGF1 overexpression represented a better prognosis, which is difficult to explain and is worthy of further study.
FN1 encodes two forms of fibronectin, soluble plasma fibronectin-1 and insoluble cellular fibronectin-1 [47]. It regulates cell adhesion and migration processes [48]. Previous studies have found that overexpressed FN1 in oesophageal squamous cell carcinoma was associated with poor prognosis, which is consistent with this study [49].
CFD is a member of the serine protease family, which stimulates the transport of triglycerides to fat cells and inhibits lipolysis. CFD is a key component in the regulation of alternative pathways [50, 51]. This study found that CFD gene expression was downregulated in TNBC and correlated with poor prognosis, which was consistent with the changes seen in gastric cancer and oral tongue squamous cell carcinoma [52, 53].