A novel metastasis–associated lncRNA destabilizes p21 through cooperative interactions with the NF90/NF45 complex

Long non-coding RNAs (lncRNA) have emerged as important regulators of gene expression at both the transcriptional and post-transcriptional levels. While altered expressions of lncRNAs have been observed in breast cancer (BCa) development, their roles in BCa progression and metastasis are still poorly understood. To identify novel BCa-associated lncRNA candidates, we have employed a high-density SNP array based approach to uncover lncRNA genes at intergenic region that are aberrantly expressed in BCa. Here we report the role of a novel lncRNA, LincIN, in breast cancer progression and metastasis. High levels of LincIN expression are frequently observed in tumors compared to adjacent normal tissues, and are strongly associated with aggressive breast cancers. Importantly, analysis of The Cancer Genome Atlas (TCGA) data further suggested that high LincIN expression was associated with poor overall survival in patients with breast cancer (P<0.05). Our gain-and-loss experiments demonstrate that LincIN play a role in tumor cell migration and invasion and knockdown of LincIN diminishes tumor cell invasion in vitro and lung metastasis in a mouse xenograft model. We also identified a LincIN-binding protein complex, NF90/NF45, through which LincIN destabilizes tumor suppressor p21 mRNA post-transcriptionally and thereby represses its protein expression. In summary, our findings delineated an oncogenic role of LincIN in breast tumor progression-metastasis, and mechanistically uncovered its cooperative actions with NF90/NF45 in regulating tumor suppressor gene expression at the post-transcriptional level. Stable lines expressing empty GFP vector or LincIN shRNAs (1 or 2) were generated using MDA-MB-231-Luc-D3H1 cells. And total RNAs were collected from vector control and shRNA cells in two independent experiments. After examining the RNA qualities by Bioanalyzer, we performed unbiased transcriptome analysis using GeneChip® Human Gene 2.0 ST Arrays. The bioinformatics tool provided by the Affymatrix will be used in our computations.