Abstract PD6-1: The long noncoding RNA M41 promotes aggressiveness and tamoxifen resistance in ER-positive breast cancers
Authors: Feng Felix Y , Ma Teng , Speers Corey , Iyer Matthew K , Zhao Shuang , Prensner John R , Rae James M , Pierce Lori J , Chinnaiyan Arul M 
Published: May 2015

Abstract
Background: Long noncoding RNAs (lncRNAs) have recently been associated with the development and progression of a variety of human cancers. To date, the interplay between known oncogenic drivers, such as estrogen receptor (ER), and lncRNAs has not been well described. In this study, we identify M41 as the top outlier lncRNA in ER-positive vs ER-negative breast cancer and investigate its role in preclinical cancer phenotypes and clinical outcomes.
Methods and Materials: RNA sequencing was performed on 89 breast cancer samples and cell lines, including 42 ER+ cases, and a modified cancer outlier analysis was used to identify lncRNAs enriched in ER-positive disease. To assess ER regulation of the top enriched lncRNA (M41), ChIP-Seq and ChIP-PCR was used to detect binding of ER to M41 promoter and qPCR was used to determine changes in M41 expression following 10 nM estradiol treatment in MCF7 and T47D cells. Following knockdown via siRNA, the impact of M41 expression was assessed on cell invasion, migration, proliferation, and anchorage-independent growth. The impact of M41 knockdown on tamoxifen sensitivity was assessed by cell proliferation studies in MCF7 cells with acquired tamoxifen resistance. Lastly, clinical associations between M41 expression and grade/node status, as well as event-free survival (EFS), was determined using ANOVA and Kaplan-Meier analyses of TCGA samples.
Results: M41, an uncharacterized lncRNA located on chr21q22.2, was identified as the top outlier lncRNA in ER-positive vs ER-negative breast cancer. M41 demonstrated outlier expression (RPKM values&gt;50) in 15% of ER-positive cancers, and was not significantly expressed in normal breast tissue. ChIP studies show that ER robustly binds to the M41 promoter. Estradiol stimulation significantly increased M41 expression in a time-dependent manner. Knockdown of M41 significantly inhibited all assessed oncogenic phenotypes in the ER-positive MCF7 and T47D cells, with a 60-80% decrease in both invasion and anchorage-independent growth, but had no effect in the ER-negative MDA-MB-231 cell line (which has minimal M41 expression). M41 expression was greater than 10-fold higher in tamoxifen-resistant MCF7 cells compared to parental controls (p&lt;0.001), and knockdown of M41 restored tamoxifen sensitivity on cell proliferation studies; studies on the mechanism of M41-mediated tamoxifen resistance are ongoing. M41 overexpression was significantly correlated with node positivity, increasing grade, and luminal B subtype in ER-positive breast cancer samples (p&lt;0.001). In TCGA samples, M41 overexpression was significantly associated with decreased EFS (p=0.003).
Conclusion: We have identified M41 as an ER-associated oncogenic lncRNA that contributes to preclinical cancer phenotype, promotes tamoxifen resistance in cell line models, and associates with poor outcomes in clinical samples. We suggest that M41 represents a novel biomarker candidate for the prognosis of ER-positive breast cancers and provides new insight into the biological complexity of breast tumor biology.
Citation Format: Felix Y Feng, Teng Ma, Corey Speers, Matthew K Iyer, Shuang Zhao, John R Prensner, James M Rae, Lori J Pierce, Arul M Chinnaiyan. The long noncoding RNA M41 promotes aggressiveness and tamoxifen resistance in ER-positive breast cancers [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr PD6-1.