Weighted correlation network analysis of triple-negative breast cancer progression: Identifying specific modules and hub genes based on the GEO and TCGA database

Abstract

Triple-negative breast cancer (TNBC) represents an aggressive malignancy of frequent high histologic grade with no effective specific targeted therapies. The present study aimed to identify specific modules and hub genes that may influence the progression of TNBC. The key words 'breast cancer' were used to search microarray datasets in the Gene Expression Omnibus and The Cancer Genome Atlas databases that included 5 datasets. A total of 11 co-expression modules were constructed based on the expression levels of 5,782 genes obtained from 456 patients with TNBC using the weighted correlation network analysis (WGCNA). The results demonstrated that the red module was significantly associated with relapse-free survival (RFS) in patients with TNBC [hazard ratio (HR)=0.381, 95% confidence interval (CI), 0.183-0.793; P=0.010]. The functional enrichment analysis revealed that the biological processes corresponding to the red module were 'mRNA processing', 'histone lysine methylation' and 'regulation of TOR signaling'. In addition, Hedgehog signaling pathways were considered to serve a critical role in the development of this disease (P<0.001). A total of 12 hub genes were identified, of which α-thalassemia/mental retardation syndrome X-linked (ATRX) was significantly associated with RFS in patients with TNBC (HR=0.601; 95%CI, 0.376-0.960; P=0.033). The receiver operating characteristic curve indicated that ATRX could distinguish relapse from non-relapse in patients with TNBC (area under the curve=0.570; P=0.023). In conclusion, the present study demonstrated that ATRX was associated with TNBC progression, which suggested that ATRX may be involved in a recombination-mediated telomere maintenance mechanism.

Keywords: hub genes; progression; triple-negative breast cancer; weighted gene co-expression network analysis; α-thalassemia/mental retardation syndrome X-linked.

Figure 1.

Flow diagram of dataset collection process. GEO, Gene Expression Omnibus; TCGA, The Cancer Genome Atlas; WGCNA, weighted correlation network analysis.

Figure 2.

(A) Determination of soft-thresholding power in WGCNA. (B) Dendrogram of the genes modules based on a dissimilarity measure. (C) Heatmap of the correlation between module eigengenes and clinical characteristics of TNBC: Each row corresponds to a module eigengene and each column corresponds to a clinic characteristic. Each cell contains the corresponding correlation and P-value. The red key represents a positive correlation between modules and clinical variables, while the blue key represents opposite. (D) Distribution of mean gene significance and standard deviation in the modules associated with pathological stage of TNBC. TNBC, triple-negative breast cancer; WGCNA, weighted correlation network analysis.

Figure 3.

Survival analysis between module eigengenes and RFS in patients with TNBC. (A) Forest plot of hazard ratios in each module for RFS (B) Kaplan-Meier analysis of RFS for the red module. CI, confidence interval; HR, hazard ratio; RFS, relapse-free survival.

Figure 4.

Visualization of the weighted gene correlation network in the red module: Cytoscape analysis identified 12 hub genes that are highlighted in bold and yellow.

Figure 5.

Association between mRNA expression of hub genes and relapse-free survival in patients with TNBC. HR, hazard ratio; TNBC, triple-negative breast cancer.

Figure 6.

Comparison between non-relapse and relapse of hub genes in patients with TNBC. (A) Boxplots of mRNA expression in ATRX, CHD9 and TRIM23 between non-relapse and relapse groups of patients with TNBC: 413 TNBC samples were divided into two groups according to tumor relapse occurrence. (B) ROC curves: AUC was calculated to evaluate the diagnostic efficiency of ATRX to distinguish between relapse and non-relapse in patients with TNBC. CHD9, chromodomain helicase DNA binding protein 9; ATRX, α thalassemia/mental retardation syndrome X-linked; AUC, area under the curve; ROC, receiver operating characteristic; TNBC, triple-negative breast cancer; TRIM23, tripartite motif containing 23.