Abstract LB-149: A novel strategy to inhibit CpG island hypermethylation and restore BRCA1 expression

Abstract

Abstract BRCA1 promoter methylation is observed in 20-60% of sporadic triple negative breast cancer (TNBC) and may be an important mechanism contributing to the loss of BRCA1 function in sporadic TNBC and other cancers with low BRCA1 expression. Demethylation and consequent reactivation of tumor suppressor genes are rational approaches being used in the treatment of cancer. However, currently available nucleoside-based DNMT inhibitors affect genome-wide DNA methylation and cannot specifically target tumor suppressor genes like BRCA1. Here, we describe a novel approach to modulate local DNA methylation by silencing a neighboring long non-coding RNA (lncRNA) which tethers DNMT1 at the BRCA1 genomic locus. The human genomic region encompassing the BRCA1 gene is complex and includes two protein coding genes (BRCA1 and NBR1), a non-coding RNA gene (NBR2), and a pseudogene of BRCA1 (BRCA1P1), within a ∼170kb region of chromosome 17q21. The BRCA1 gene on the minus strand is located head-to-head with NBR2 on the plus strand, whereas BRCA1P1 on the minus strand is located head-to-head with NBR1 on the plus strand. The promoter between the BRCA1 and NBR2 genes and that between the BRCA1P1 and NBR1 genes are bidirectional, expressing transcripts in opposite directions through convergent transcription. The BRCA1P1 pseudogene was generated by a recent evolutionary event: partial duplication of BRCA1 gene followed by insertion of a processed pseudogene of RPLP1. It expresses a chimeric lncRNA retained in nuclei. Interference with the nuclear expression of BRCA1P1 lncRNA using a specific anti-sense oligonucleotide (ASO) decreased the promoter methylation of BRCA1 and increased BRCA1 expression. RNA immunoprecipitation (RIP) assays revealed DNMT1 interactions with BRCA1 mRNA and BRCA1P1 lncRNA at the locus. Chromosome conformation capture (3C) will assess whether there is a long-range interaction between the BRCA1 and BRCA1P1 promoters through DNMT1 and mediators. Our data support a long-range cis-regulation of BRCA1 expression by neighboring BRCA1P1 lncRNA through an interaction with DNMT1 at the locus. Depleting BRCA1P1 with ASO could be developed as a therapeutic method to inhibit BRCA1 promoter methylation and restore BRCA1 expression. Citation Format: Yoo Jeong Han, Jing Zhang, Aleix Prat, Toshio Yoshimatsu, Maria Gomez-Vega, John Kwon, Charles M. Perou, Prasanth Kannanganattu, Olufunmilayo I. Olopade. A novel strategy to inhibit CpG island hypermethylation and restore BRCA1 expression. [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 LB-149. doi:10.1158/1538-7445.AM2015-LB-149