Identification of lncRNAs associated with breast cancer prognosis from Latina America patients

Breast cancer (BC) is the most common cause of female cancer-related death worldwide and is considered a public health problem. Many functional studies have shown that long noncoding RNAs (lncRNAs) play different roles in gene expression regulation, acting as epigenetic factors. Accumulating evidence indicates that lncRNAs modulate diverse biological processes, and their altered expression is associated with the development and progression of cancer, including BC. Here, aiming to identify lncRNAs associated with breast cancer, we performed a re-analysis of the expression data from 1,071 tumors of eligible patients in the project LACRN MPBCS (Latin American Cancer Research-Network - Molecular Profile of Breast Cancer Study). Using normalized data, we compared the expression profiles of triple-negative breast cancer (TNBC; 170 cases) and non-TNBC tumors (782 cases). A total of 59 differentially expressed lncRNAs (DElncRNAs) could be identified based on the criteria of |log2FC| > 1 and FDR < 0.05, using the DESeq2 R package. In the Kaplan-Meier survival analysis, we identified DElncRNAs that affect disease-free survival and/or overall survival, with 8 in TNBC and 26 in non-TNBC patients. Further, we used multivariate Cox proportional-hazards models to evaluate independent predictors of survival. Two of those DElncRNAs, VLDLR-AS1 and PART1, were independent prognostic markers for TNBC patients, and seven, LINC00239, FAM30A, LINC00842, LINC01315, EGOT, LY6E-DT, and SLC25A21-AS1, were independent prognostic markers for non-TNBC patients. Our study identifies several lncRNAs that might participate in tumor progression and may serve as candidate biomarkers for BC.