Abstract GS2-01: Discovery and characterization of an estrogen bound LncRNA in late-Stage breast cancer
Authors: Maher CA , Silva-Fisher J , Eteleeb A , Tang C , Perou C , Reis-Filho JS , Mardis ER , Ellis MJ 
Published: February 2018

Breast cancer is the second most common newly diagnosed cancer and the second leading cause of cancer death among women in the United States. Despite the proven benefits of adjuvant endocrine therapy in women with hormone receptor positive breast cancer, relapses still occur over 5 years after initial treatment with endocrine therapy, referred to as late-stage relapse. Currently, the mechanisms of driving late-stage relapse are poorly characterized. To date, breast cancer research has primarily focused on protein-coding genes thereby missing the emerging class of long intergenic non-coding RNAs (lncRNAs) that may serve as critical regulators of relapse. Furthermore, the current understanding of lncRNA function is still in its infancy representing a critical gap for translating lncRNA discoveries into real-world applications to benefit patient care. Several well-described examples indicate that lncRNAs may be master epigenetic regulators in cancer biology through their interactions with proteins regulating target gene expression. Therefore, we hypothesize that lncRNAs may interact with estrogen receptor alpha 1 (ESR1) to regulate genes promoting late-stage relapse. To address this, we performed a transcriptome analysis of tumors from a unique cohort of 24 patients that had late-stage relapse to discover a novel set of lncRNAs, most of which have not yet been characterized. Next, we used RNA Immunoprecipitation coupled with transcriptome sequencing (RIP-Seq) to identify transcripts bound to ESR1 in T47D cells. We discovered 217 lncRNAs bound to ESR1 of which 50 were up-regulated in late-stage breast cancer. We chose to focus the most up-regulated lncRNA in late-stage relapse. Since it is an unannotated lncRNA we will refer to it as 'LAte-Stage relapse ESR1-Bound lncRNA 1', or LASER-1. To further understand the interplay between LASER-1 and ESR1, cells endogenously expressing LASER-1 were subjected to partial digestion to preserve lncRNA and protein interactions. Protected RNA fragments were subsequently immunoprecipitated with ESR1 and quantified by qPCR to reveal specific ESR1 interaction sites within LASER-1. Next, we observed increased expression of LASER-1 in ER+ breast cancer cell lines. Notably, LASER-1 expression was elevated in MCF7 long-term estrogen deprived (MCF7 LTED) cells -- that have amplified ESR1 -- relative to parental MCF7 cells. To demonstrate that LASER-1 promotes oncogenic phenotypes we transiently silenced LASER-1 in two cell lines with high endogenous expression of LASER-1 (including MCF LTED) and observed a decrease in cellular proliferation and invasion. Subsequent gene expression analysis after silencing LASER-1 altered mRNA and protein levels of critical cell cycle genes (i.e., p27). Overall, this is the first study to discover ESR1 bound lncRNAs that may be contributing to late-stage relapse in breast cancer. In the short-term, our ongoing research may lead to significant breakthroughs establishing the importance of LASER-1 as a master regulator in late-stage relapse. In the longer-term, we envision this research may lead to the development of novel therapeutics targeting LASER-1 with the potential for rapid clinical translation.

Citation Format: Maher CA, Silva-Fisher J, Eteleeb A, Tang C, Perou C, Reis-Filho JS, Mardis ER, Ellis MJ. Discovery and characterization of an estrogen bound LncRNA in late-Stage breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr GS2-01.