Aggressive breast cancer is difficult to treat as it is unresponsive to many hormone-based therapies; therefore, it is imperative to identify novel, targetable regulators of progression. Long non-coding RNAs (lncRNAs) are important regulators in breast cancer and have great potential as therapeutic targets; however, little is known about how the majority of lncRNAs function within breast cancer.
Here, researchers at the University of Vermont College of Medicine characterize a novel lncRNA, MANCR (mitotically-associated long non-coding RNA; LINC00704), which is upregulated in breast cancer patient specimens and cells. Depletion of MANCR in triple-negative breast cancer (TNBC) cells significantly decreases cell proliferation and viability, with concomitant increases in DNA damage. Transcriptome analysis, based on RNA sequencing (RNA-seq), following MANCR knockdown reveals significant differences in the expression of >2000 transcripts, and gene set enrichment analysis (GSEA) identifies changes in multiple categories related to cell cycle regulation. Furthermore, MANCR expression is highest in mitotic cells by both RT-qPCR and RNA in situ hybridization. Consistent with a role in cell cycle regulation, MANCR-depleted cells have a lower mitotic index and higher incidences of defective cytokinesis and cell death. Taken together, these data reveal a role for the novel lncRNA, MANCR, in genomic stability of aggressive breast cancer, and identify it as a potential therapeutic target.
Depletion of MANCR affects gene expression
A) MA plot displaying differentially expressed mRNAs (blue circles) and lncRNAs (red circles) in MDA-MB-231 MCR-17-0548 with MANCR knockdown (MANCR ASO_2) compared to control MDA-MB-231 cells (Control ASO); gray dots represent genes that did not make the fold change (≥1.5) or p-value (<0.05) cutoffs. Data is from three biological replicates. B) Top 20 gene sets and their normalized enrichment scores (NES) from gene set enrichment analysis of differentially expressed mRNAs using the Molecular Signatures Database (MSigDB) Hallmark gene sets. C) The number of genes with either increased (upper panel) or decreased (lower panel) expression (fold change ≥1.5) in both MANCR ASO_2 vs Control and MCF-10A vs MDA-MB-231 cells. D) Heatmaps showing the expression of the 79 genes (rows) in the MSigDB “Biological Processes: Regulation of Chromosome Segregation” gene set (left panel) and the 136 genes in the “Biological Processes: DNA Packaging” gene set (right panel) for MDA-MB-231, Control ASO, MANCR ASO_2, and MCF-10A cells (columns). The color scale of the heatmaps represents the relative expression of each gene.