Breast cancer is one of the most prevalent cancers and is a complex and heterogeneous group of diseases that arises in mammary glands due to a variety of somatic mutations and epigenetic changes that characterize individual tumors. The estrogen receptor (ER), particularly ER-?, is a well-studied driver of breast cancer and serves as both a strong prognostic marker and a predominant therapeutic target. In fact over 60% of all breast cancers are ER positive. ER functions as a ligand-dependent transcription factor, binding genomic estrogen response elements to either activate or repress the transcription of target genes. Most studies of ER-positive breast tumors and cell lines have focused on proteins regulated by ER as potential modulators of tumor progression, largely overlooking the possible role of non-coding RNAs in tumor formation. Long noncoding RNAs (lncRNAs) have emerged as an important class of genes involved in many cellular processes and have been implicated in biological, developmental, and pathological processes. Several human lncRNAs have already been shown to be integral players in cancer progression, including HOTAIR in breast cancer and SCHLAP1 and PCAT1 in prostate cancer. However, lncRNAs have not yet been shown to play a role in mediating ER-driven breast cancer. Investigating the role of lncRNAs in ER driven cancers is an exciting avenue for further understanding the mechanisms of breast cancer progression. Our preliminary data have identified an intriguing ER associated lncRNA, BRCAT431, that is differentially expressed in breast cancer, transcriptionally responsive to estrogen stimulation, confers transformative phenotype in breast cancer cell lines, and binds the protein hnRNPL. Preclinical, clinical, and mechanistic investigation of this lncRNA is outlined in this proposal.
Specific Aim 1 : Characterize preclinical and clinical phenotype of BRCAT431. We will investigate the oncogenic potential of in in vivo mouse xenograft studies. We will also assess the association of BRCAT431 with poor clinical outcomes through interrogation of clinical datasets bearing expression data for the lncRNA.
Specific Aim 2 : Functional characterization of BRCAT431 and hnRNPL interaction. We have shown that the two molecules physically interact and aim to characterize the functionality of this interaction. We propose to identify overlap in the genes whose expression is regulated by hnRNPL and BRCAT431. Additionally we will localize and delete the binding site of hnRNPL on BRCAT431, and subsequently overexpress mutant BRCAT431 lacking hnRNPL binding to assess the function of the binding interaction.
Specific Aim 3 : Assess the affect of BRCAT431 on the RNA binding profile of hnRNPL. Given that hnRNPL is a known regulator of RNA splicing and stability, in order to further investigate the functional relationship between BRCAT431 and hnRNPL, we will perform CLIP-seq with and without BRCAT431 knockdown to characterize the effect of BRCAT431 on the RNA binding profile of hnRNPL.

Public Health Relevance

Breast cancer is one of the most common cancers in the U.S. and a leading cause of cancer death, with estrogen Receptor (ER) being the predominant cancer driver in over 60% of breast cancers. Most studies attempting to understand the role of ER in cancer have focused on its interaction with other protein-coding genes. In this study, we aim to discover and investigate a long non-coding RNA implicated in breast tumor estrogen responsiveness and interrogate its functional and mechanistic role in breast cancer.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Individual Predoctoral NRSA for M.D./Ph.D. Fellowships (ADAMHA) (F30)
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Special Emphasis Panel (ZRG1)
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Damico, Mark W
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University of Michigan Ann Arbor
Schools of Medicine
Ann Arbor
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Hosono, Yasuyuki; Niknafs, Yashar S; Prensner, John R et al. (2017) Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA. Cell 171:1559-1572.e20
Niknafs, Yashar S; Pandian, Balaji; Iyer, Hariharan K et al. (2017) TACO produces robust multisample transcriptome assemblies from RNA-seq. Nat Methods 14:68-70
Niknafs, Yashar S; Han, Sumin; Ma, Teng et al. (2016) The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression. Nat Commun 7:12791