The identification of novel long non-coding RNAs and immune-related long non-coding RNAs in triple-negative breast cancers

Long non-coding RNAs have been widely studied in Triple-Negative Breast Cancers (TNBCs), but from the previous studies, it is seen that study about the association of lncRNAs with the subtypes of TNBCs has been very limited. Similarly, research on immune lncRNAs in TNBCs has not been well studied previously. Here, in this study initially by analyzing RNA-seq data from 361 TNBC samples (317 tumor and 44 normal samples), we have identified 5,716 novel lncRNAs and characterized them along with annotated lncRNAs. Differentially expressed lncRNAs specific to the subtypes of TNBCs were detected. Among them, many of the upregulated lncRNAs were enriched in co-expressed modules with protein-coding genes related to DNA replication, B-cell receptor pathway, Focal adhesion, and other metabolic processes related to subtypes of TNBCs. We also identified 602 immune lncRNAs in TNBCs that were associated with immune pathways, positively correlated with immune cells, and negatively correlated with tumor purity. TNBCs were classified into two immune clusters Immune-High (IH) and Immune-Low (IL) based on 602 immune lncRNAs expression. Immune lncRNA LINC01215 and MSTRG_243701 (novel lncRNA) were further identified as the most important signature lncRNAs related to the Immune-High cluster, based on the results from the machine learning approaches. Thus, these results give us valuable information about lncRNA function in the subtypes of TNBCs and how they may contribute to the shaping of the immune environment in TNBCs.