Targeting heterochromatic RNAs in high risk breast cancer

Institution: Salk Institute for Biological Studies
Investigator(s): Tony Hunter, Ph.D. -
Award Cycle: 2017 (Cycle 23) Grant #: 23IB-0016 Award: $291,000
Award Type: IDEA
Research Priorities
Biology of the Breast Cell>Pathogenesis: understanding the disease



Initial Award Abstract (2017)

Non-technical overview of the research topic and relevance to breast cancer: The survival rate of breast cancer patients has dramatically improved over the last two decades due to advances in diagnostics and therapeutics. However, a subpopulation where these advances are lacking are those individuals with a high risk for breast cancer due to genetic predisposition, such as mutations in BRCA1. Although identification of BRCA1 has led to a diagnostic tool for detection of mutations in the gene, BRCA1 mutated breast cancers remain highly aggressive and occur at young age of affected women. The evidence of a BRCA1 mutation has not yet allowed patients to be treated in more effective ways other than increased monitoring or radical measurement of prophylactic mastectomies. Therefore, understanding the mechanism of BRCA1 functioning as a tumor suppressor is critical in developing more effective treatments of familial breast cancer. New biomarkers that represent a functional loss of BRCA1 protein would promise early detection of the tumor onset thereby warranting more effective treatment. Furthermore, BRCA1 has also been shown to be mutated in sporadic breast cancers, and BRCA1-mutated breast cancer shares a number of pathological characters with a much larger group of hormone receptor negative breast cancers for which the targeted therapy is also lacking. Emerging evidence reveals that BRCA1 epigenetically controls the expression of noncoding RNAs, including oncogenic microRNAs and satellite RNA. We and others have shown that non-coding satellite RNAs are aberrantly overexpressed in BRCA1-mutant breast tumors and a number of other human epithelial malignancies. In this proposal, we are investigating the role of satellite RNA in causing breast tumor formation and determine what factors are required for the action of satellite RNA in tumorigenesis.

The question(s) or central hypotheses of the research: Overexpression of heterochromatic satellite RNAs promotes tumorigenesis by binding and sequestering factors important for maintaining genomic integrity.

The general methodology: To test our central hypothesis, we will establish two complementary mouse models to examine the tumorigenic potential of the heterochromatic satellite RNAs. We will use a proteomic approach to address why satellite RNA overexpression, which is one of the immediate consequences of loss of the BRCA1 function, will lead to genomic instability and tumor formation.

Innovative elements of the project and potential impact: In this proposal, we use innovative animal models and a proteomic approach to determine novel ways by which disruption of the most silenced portion of the mammalian genome leads to cancer formation. The proposal is strongly supported by the preliminary data, the expected outcome will dramatically advance our understanding of non-coding RNAs expressed from the heterochromatin. It represents a new line of investigation in breast cancer research and has a potential to lead to a breakthrough in the field. The establishment of the satellite-RNA transgenic mouse models and validation and characterization of satellite RNA-binding proteins will improve our understanding of inherited and high risk breast cancer beyond an incremental advancement. The success of the proposal would have a significant clinical impact for patients with BRCA1 mutations by paving the way to develop satellite RNAs as a novel biomarker for early diagnosis. The acquired data will be critical for us to apply for more substantial funding to support large scale clinical investigations that move our research beyond cell lines and mouse models based tools.




Progress Report 1 (2018)

The survival rate of breast cancer patients has dramatically improved over the last two decades due to advances in diagnostics and therapeutics. However, effective targeted treatments are still not available to patients with triple-negative breast cancers as well as patients carrying mutations in the tumor suppressor gene BRCA1. People who have inherited mutations in BRCA1 tend to develop breast cancers at young ages and BRCA1-mutant breast cancers remain highly aggressive. Therefore, understanding the mechanism of BRCA1 function as a tumor suppressor is vital to develop more effective treatments to BRCA1 mutant cancers and triple-negative breast cancers, which share a number of pathological characteristics. Emerging evidence reveals that BRCA1 epigenetically controls the expression of non-coding RNAs, including oncogenic microRNAs and satellite RNA. Our group and others have previously shown that non-coding satellite RNAs are aberrantly overexpressed in BRCA1-mutant breast tumors and a number of other human epithelial malignancies.

In this proposal, we planned to investigate the role of satellite RNA in promoting breast cancer formation and determine what factors are required for the action of satellite RNA in tumorigenesis. We have accomplished the majority of specific aims initially proposed in the grant. One particular barrier we have encountered is the generation of one of two designed mouse models, which are the conditional mice that allow inducible expression of satellite RNA in the mammary gland using the Krt14-Cre. While this work is still in progress, we have shown that: 1) expression of satellite RNA, either provided exogenously or activated endogenously, directly induces the DNA damage response and chromosome instability; 2) overexpression of satellite RNA in conjunction with shRNA against the tumor suppressor gene p53 in mammary gland via intraductal viral injection leads to breast cancer in mice, demonstrating the oncogenic potential of satellite RNA. To understand the molecular mechanisms underlying satellite RNA induced genomic instability effects, we further demonstrated that: 3) satellite RNA interacts with the BRCA1 associated protein network; 4) satellite RNA expression interferes with the BRCA1 dependent function in DNA replication fork protection leading to elevated RNA-DNA hybrid formation, which is necessary for satellite RNA induced DNA damage and genomic instability. In summary, we have demonstrated that aberrant expression of satellite RNA can promote breast cancer formation by interacting with BRCA1 associated protein network required for replication fork protection and genomic integrity. These studies lay the foundation for developing novel therapeutic strategies that block the effects of non-coding satellite RNAs in cancer cells. To this end, we plan to extend this project by pursuing a therapeutic approach to specifically target satellite RNAs. We have established the collaboration with Ionis Pharmaceuticals, a leading biopharmaceutical company in RNA- targeted drug discovery and development. We have obtained two sets of modified antisense oligonucleotides (ASO) designed against satellite RNA. We are currently in the process of screening these ASOs and further characterization by functional tests. In the next funding cycle, we aim to identify specific and effective ASOs in order to validate ASO as a potential therapeutic approach toward breast cancer.