SAN ANTONIO, TX—In the largest reported compendia of breast cancer long noncoding RNAs (lncRNAs), BRCAT431 was identified as the top lncRNA upregulated in ER-positive breast cancers, and a novel mechanism by which this lncRNA functions was also identified. These findings suggest that BRCAT431 promotes tamoxifen resistance, thereby increasing the clinical risk of recurrence and metastases in breast cancer, according to a study presented at the 2015 San Antonio Breast Cancer Symposium.1

“Overall, this study supports the rationale for investigating lncRNAs as novel biomarkers and therapeutic targets in breast cancer,” said Felix Y. Feng, MD, of the University of Michigan Medical School.

Previously, Feng’s team performed an informatics-based analysis on 7256 RNA sequencing (RNA Seq) libraries from tumors, normal tissues, and cell lines specimens to delineate the landscape of lncRNAs in the human transcriptome. The analysis identified 58 648 lncRNAs, including more than 45 000 novel transcripts. Interrogation of this lncRNA compendium identified top candidate estrogen receptor (ER)-associated lncRNAs in breast cancer and characterized their association with disease progression, Feng explained.

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Sample set enrichment analysis (SSEA) was performed on more than 1000 RNA Seq libraries from breast cancer and normal tissue samples from The Cancer Genome Atlas project. This analysis nominated breast cancer associated transcript 431 (BRCAT431) as a top outlier lncRNA in ER+ breast cancers. BRCAT431 expression is associated with signatures of aggressive disease and is increased in the luminal B subtype of breast cancer.

In vitro experiments demonstrate that siRNA-mediated knockdown of BRCAT431 inhibits oncogenic phenotypes in cell lines. Tamoxifen resistance was associated with significantly increased BRCAT431 levels in both MCF7 and T47D cells, and this resistance was revised with knockdown of BRCAT431. In vivo xenograft and CAM studies demonstrate that xenograft growth and tumor invasion was also decreased by more than 50% with knockdown of BRCAT431. RNA pulldown followed by mass spectrometry nominated the RNA binding protein hnRNPL as a top BRCAT431 interactor. A 27-base region of BRCAT431 necessary for its interaction with hnRNPL was identified with deletion studies. This loss reversed BRCAT431-induced invasion. Finally, in guilt-by-association studies, a strong association between BRCAT431 overexpression and tumor grade, recurrence, and metastases was identified.

The study findings identified BRCAT431 as a top outlier lncRNA in ER+ breast cancer. It is associated with aggressive clinical and preclinical phenotypes. Mechanistically, BRCAT431 interacts with HnRNPL to promote disease aggressiveness. “LncRNA should be explored as biomarkers and therapeutic targets in cancer,” said Feng.


1. Feng FY, Niknafs Y, Han S, et al. Interrogating the landscape of long noncoding RNAs in breast cancer to identify predictors of tamoxifen resistance. Oral presentation at: San Antonio Breast Cancer Symposium; December 8-12, 2015; San Antonio, TX.