Disrupting long noncoding RNA methylation to elicit antimorph behavior in breast cancer

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PROJECT SUMMARY Specific long noncoding RNAs (LncRNAs) that are overexpressed in breast cancer aid in diagnosis and promote molecular mechanisms that drive breast cancer progression. Our recent work has identified a breast- cancer associated LncRNA that converts from an oncogene to a tumor suppressor by mutation of one single nucleotide. This “antimorphic” effect is caused by the prevention of RNA methylation at this one site, allowing overexpression of the converted LncRNA to decrease cancer phenotypes more so than depletion of the wild- type version. This exciting new finding prompts us to delve deeper into how this is occurring, with the ultimate goald of specifically disrupting this m6A pathway as a novel therapeutic approach. Proposed therapeutic intervention for breast cancer-associated LncRNAs has mainly been aimed at depleting the cancer-promoting RNA, with the assumption that this would be the most effective approach to reduce cancer phenotypes. Our results suggest a novel therapeutic approach to oncogenic LncRNAs, where disruption of RNA methylation alone has a greater impact than simple elimination of the RNA. The current proposal provides a roadmap to understand how to elicit antimorphic effects in an oncogenic LncRNA. We aim to use this proof-of-principle project as a springboard for future work that would lead this therapeutic approach to the clinic. We hypothesize that m6A modification sites on a specific breast cancer-associated LncRNAs can be targeted and disrupted to reverse oncogenic behavior below baseline, providing a roadmap for a potential new therapeutic approach. In our first aim, a mutant HOTAIR LncRNA that behaves as an antimorph will be studied for physical interactions in triple negative MDA-MB-231 breast cancer cells using proteomic approaches. Physical and functional interactors will then be depleted in a breast cancer cell line that overexpresses the antimorph HOTAIR to determine their role in the antimorph mechanism. Recently-derived primary cell lines from breast cancer patient-derived xenografts will be used to determine the generalizability of this mechanism. In the second aim, anti-sense oligonucleotides (ASOs) will be used to disrupt the m6A site on HOTAIR to elicit antimorph behavior. In a parallel approach, we will developed an optimized strategy to deliver the antimorph HOTAIR RNA directly to suppress cancer phenotypes. These two approaches are complementary in cases of breast cancer where HOTAIR is overexpressed and those where it is not. Our work would be a foundational test of a novel therapeutic approach in breast cancer by inducing antimorphic behavior of an m6A-modified LncRNA. In general, the ASO-based strategy is a novel approach to breast cancer therapeutics. RNA therapeutics are now a reality and are gaining wide acceptance. Our project capitalizes on this exciting atmosphere with an ambitious, novel approach to noncoding RNA interventions in breast cancer. By taking advantage of a molecular switch provided by m6A, we can reverse the activity of an oncogenic LncRNA to reverse breast cancer properties.