Sparse Gene Coexpression Network Analysis Reveals EIF3J-AS1 as a Prognostic Marker for Breast Cancer

Predictive and prognostic biomarkers facilitate the selection of treatment strategies that can improve the survival of patients. Accumulating evidence indicates that long noncoding RNAs (lncRNAs) play important roles in cancer progression, with diagnostic and prognostic potential. However, few prognostic lncRNAs are reported for breast cancer, and little is known about their functions that contribute to cancer pathogenesis. In this paper, we used weighted correlation network analysis (WGCNA) to construct networks containing noncoding and protein-coding genes based on their expression in 1097 breast cancer patients. The differentially expressed genes were significantly overlapped with gene modules regulating cell cycle and cell adhesion. The cell cycle-related lncRNAs were consistently downregulated in breast cancer. One lncRNA, EIF3J-AS1, is significantly associated with clinicopathological characteristics, including tumor size, lymph node metastasis, estrogen receptor (ER), and progesterone receptor (PR) status. Kaplan–Meier survival analysis revealed that EIF3J-AS1, a downregulated lncRNA in breast tumor, is a potential prognostic marker for breast cancer. EIF3J-AS1 may function in an estrogen-independent manner and could be inhibited by the compound FDI-6. Therefore, integrating sparse gene coexpression network and clinicopathological features can accelerate identification and functional characterization of novel prognostic lncRNAs in breast cancer