Abstract 2870: A novel metastasis-associating LincRNA destabilizes tumor-suppressor mRNAs through cooperative action with NF90/ILF3 binding
Authors: Jiang Zhengyu , Yan Zhou , Devarajan Karthikeyan , Slater Carolyn M. , Daly Mary B. , Chen Xiaowei 
Published: August 2015

Abstract
Background: Recent genome-wide profiling by sequencing and distinctive chromatin signatures has identified thousands of long intergenic non-coding RNA (lincRNA) species (&gt;200 nt). LincRNAs are emerging as important regulators of gene expression. While altered expressions of lincRNAs have been observed to play an important role in tumorigenesis, their roles in breast cancer (BCa) progression and metastasis are still poorly understood.
Experimental designs and results: To discover novel BCa-associated lincRNA transcripts, we have employed a high-density SNP array based approach, in which we specifically probed the transcripts in the human intergenic region to globally explore lincRNA genes that are aberrantly expressed in BCa. We found 38 lincRNA transcripts that were dysregulated in tumors (P&lt;0.01, FDR2-fold change, vs. adjacent normal samples), including 22 lincRNAs being up-regulated, and 16 lincRNAs being down-regulated. One of the lincRNAs, termed LincIN, was probed by 5 exon-targeted markers, showing significant upregulation of expression in breast tumors (P&lt;0.001). Results from BCa tissue microarray (TMA) analysis by RNAscope® ISH demonstrated that high LincIN expression in BCa tissues correlated with poorly differentiated tumor grade (vs. moderately and well differentiated grade, P&lt;0.05). Furthermore, knockdown of LincIN in BCa cells diminished cancer cell migration and invasion in vitro and reduced lung metastasis in MDA-MB-231-luc-D3H1 xenografted mice, while overexpression of LincIN tended to promote BCa cell migration in vitro. Using RNA pull-down and subsequent mass spectrometry (MS), we identified and validated that NF90/ILF3 is one of the most abundant LincIN binding partners. NF90/ILF3 is a well-known double-stranded RNA-binding protein and participates in the post-transcriptional regulation of many genes, including p21. Overexpression of LincIN in MCF10A cells significantly decreased the p21 protein level but not the static p21 mRNA level, suggesting a potential role of LincIN in post-transcriptional regulation of p21. Importantly, the effect of LincIN-mediated downregulation of p21 protein was diminished when NF90 was reduced by RNAi. These results suggested that LincIN may regulate breast tumor progression/metastasis via mediating the NF90/ILF3-associated post-transcriptional regulation.
Conclusions: Results from our clinical correlative analysis and functional studies support that LincIN is a promising prognostic RNA marker for BCa progression/metastasis. Knockdown of LincIN in BCa cells diminished cancer cell invasion in vitro and reduced lung metastasis in vivo, suggesting that LincIN could be a novel target for treating advanced BCa disease. This work was partially supported by the Susan G. Komen for the Cure (KG100274), and Eileen Stein Jacoby Fund.
Citation Format: Zhengyu Jiang, Zhou Yan, Karthikeyan Devarajan, Carolyn M. Slater, Mary B. Daly, Xiaowei Chen. A novel metastasis-associating LincRNA destabilizes tumor-suppressor mRNAs through cooperative action with NF90/ILF3 binding. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2870. doi:10.1158/1538-7445.AM2015-2870