A sense-antisense RNA interaction drives metabolic reprogramming in metastatic breast

Background: Metabolic reprogramming is a hallmark of breast cancer progression. However, the underlying regulatory pathways that initiate and maintain this process remain largely unexplored. Recently, we have identified a novel antisense RNA that helps protect breast cancer cells against oxidative stress by reprogramming their metabolic redox state. Using cell line and patient-derived xenograft models, as well as direct measurements in clinical samples, we have demonstrated the unique regulatory functions of this antisense RNA in increasing the metastatic capacity of breast cancer cells.Results: Non-coding RNAs have emerged as major drivers of metastatic progression. We have recently demonstrated that specific classes of non-coding RNAs, such as tRNAs (Goodarzi et al, Cell, 2016) and tRNA fragments (Goodarzi et al, Cell, 2015), play major roles in breast cancer metastasis as post-transcriptional regulators of gene expression. However, these types of regulatory RNAs constitute only a fraction of the non-coding RNAs that are aberrantly expressed in highly metastatic cells. For example, antisense RNAs are a large but often ignored class of RNAs with poorly understood cellular functions. We recently developed a new computational algorithm to systematically annotate antisense RNAs and identify those that are associated with metastatic progression based on data from cell line and patient-derived xenograft models, as well as matched primary and metastatic tumors from triple-negative breast cancer patients. We identified a previously unknown antisense RNA, which is transcribed from a locus in the 3’ UTR of the gene NQO1 (and is hence named NQO1-AS). Both NQO1-AS and NQO1 are significantly upregulated in highly metastatic breast cancer cells, and we have shown that the NQO1 sense mRNA is stabilized by the expression of NQO1-AS. Our results indicate that NQO1-AS forms a stable duplex with the 3’ UTR of NQO1 and induces the expression of a longer and more stable isoform of NQO1 mRNA. Metabolomic measurements in NQO1 knockdown and control cells revealed that increased NQO1 activity enables cancer cells to better tolerate the oxidative stress experienced during metastasis. We demonstrated this by performing lung metastasis assays in xenograft models. To confirm the clinical relevance of these findings, we performed comprehensive clinical association studies, and also used quantitative PCR and immunohistochemistry to measure NQO1 levels across all disease stages. We observed a highly significant association between higher NQO1 and NQO1-AS expression and metastatic relapse.Methods: We developed a method named iRAs to annotate and quantify antisense RNAs. We used global run-on assays (GRO-seq) and RNA sequencing in poorly and highly metastatic breast cancer cells to identify NQO1-AS as a novel pro-metastatic antisense RNA. We used both Gapmers and CRISPR-i to knock down NQO1-AS and to measure its impact on NQO1 mRNA stability and expression. We used CRISPRi to silence NQO1 in both MDA-231 and HCC-1806 breast cancer lines, and measured the metabolic consequences of NQO1 knockdown by measuring NADPH flux as well as performing general metabolomic profiling. We also used in vivo lung colonization assays (n=5 mice in each arm) to measure the metastatic capacity of NQO1 knockdown cells. Log-rank test (univariate) and Cox Proportional Hazard Models (multivariate) were used to perform survival analyses in METABRIC and the kmplot aggregate dataset. Mann-Whitney or ANOVA was used to compare expression of NQO1 and NQO1-AS across samples stratified based on sub-type and tumor grade/stage in public datasets as well as our own measurements in clinical samples (n=96; 5 healthy, 23 stage I, 30 stage II, 29 stage III, and 9 stage IV). IHC was performed on tissue microarrays from CHTN (Breast Progression), and blinded scoring was used to assess NQO1 levels. Citation Format: Hani Goodarzi, Bruce Culbertson, Kristle Garcia, Lisa Fish. A sense-antisense RNA interaction drives metabolic reprogramming in metastatic breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS19-01.