Triple-negative breast cancer (TNBC) is the deadliest form of breast cancer. Unlike other types of breast cancer that can be effectively treated by targeted therapies, no such targeted therapy exists for all TNBC patients. The ADAR1 enzyme carries out A-to-I editing of RNA to prevent sensing of endogenous double-stranded RNAs. ADAR1 is highly expressed in breast cancer including TNBC. Here, we demonstrate that expression of ADAR1, specifically its p150 isoform, is required for the survival of TNBC cell lines. In TNBC cells, knockdown of ADAR1 attenuates proliferation and tumorigenesis. Moreover, ADAR1-knockdown leads to robust translational repression. ADAR1-dependent TNBC cell lines also exhibit elevated IFN stimulated gene expression. IFNAR1 reduction significantly rescued the proliferative defects of ADAR1 loss. These findings establish ADAR1 as a novel therapeutic target for TNBC tumors.

14Triple-negative breast cancer (TNBC) is the deadliest form of breast cancer. Unlike other 15 types of breast cancer that can be effectively treated by targeted therapies, no such targeted 16 therapy exists for all TNBC patients. The ADAR1 enzyme carries out A-to-I editing of RNA to 17 prevent sensing of cellular double-stranded RNAs (dsRNA). ADAR1 is highly expressed in 18 breast cancer including TNBC. Here, we demonstrate that ADAR1 expression and editing 19 activity is required in TNBC cell lines but not in ER+ and/or Her2+ cells. In TNBC cells, 20 knockdown of ADAR1 attenuates proliferation and tumorigenesis. PKR expression is elevated in 21 TNBC and its activity is induced upon ADAR1-knockdown, which correlates with a decrease in 22 translation. ADAR1-dependent TNBC cell lines also exhibit elevated IFN stimulated gene 23 expression. IFNAR1 reduction significantly rescues the proliferative defects of ADAR1 loss. 24These findings establish ADAR1 as a novel therapeutic target for TNBC tumors. 25 26 Keywords: ADAR1, triple-negative breast cancer, RNA editing, Type I IFN, PKR 27 28 65highlighting the therapeutic potential of ADAR1 inhibitors for the treatment of TNBC. 66 Results 67ADAR1 is highly expressed in all breast cancer subtypes 68 Using publicly available data from TCGA (The Cancer Genome Atlas) (Han et al., 2015, 69 Fumagalli et al., 2015, we found that high expression of ADAR1 correlated with poor prognosis 70 of breast cancers ( Figure 1A). Recent studies indicated that ADAR1 promotes tumorigenesis of 71 metaplastic breast cancers, and that high expression of ADAR1 correlates with poor prognosis in 72 basal-like breast cancers (Sagredo et al., 2018, Dave et al., 2017. Since both basal-like and 73 5 metaplastic breast cancers share similar characteristics with TNBC, we sought to determine the 74 importance of ADAR1 in the tumorigenesis of TNBC. By evaluating the TCGA database, we 75 found that while mRNA expression of ADAR1 was higher in TNBC compared to normal, it was 76 not significantly different between TNBC and non-TNBC tumors ( Figure 1B). Additionally, 77 ADAR1 expression was not significantly higher in any one subtype of breast cancer based on 78 PAM50 classification(Lehmann et al., 2016) (Supplemental Figure 1A). This observation is 79 consistent with data from the Cancer Cell Line Encyclopedia (CCLE), which uses both RNA-seq 80 and Reverse Phase Protein Array (RPPA) to determine RNA and protein expression levels in 81 numerous cancer cell lines (Supplemental Figure 1B-C). Data from both the TCGA and CCLE 82 datasets also revealed that both p150 and p110 isoforms of ADAR1 were expressed at similar 83 levels between TNBC and non-TNBC specimen (Supplemental Figure 1D-H), with p110 84 expression being consistently higher than p150 in all samples. Additionally, we assessed p150 85 isoform expression by immunohistochemistry in TNBC and non-TNBC patient tumors, Figure 86 1D. We sought to determine the protein expression level of the ADAR1-p150 isoform in a panel 87 of established breast ca...

Detection of viral double-stranded RNA (dsRNA) is an important component of innate immunity. However, many endogenous RNAs containing double-stranded regions can be misrecognized and activate innate immunity. The interferon inducible ADAR1-p150 suppresses dsRNA sensing, an essential function for ADAR1 in many cancers, including breast. Although ADAR1-p150 has been well established in this role, the functions of the constitutively expressed ADAR1-p110 isoform are less understood. We used proximity labeling to identify putative ADAR1-p110 interacting proteins in breast cancer cell lines. Of the proteins identified, the RNA helicase DHX9 was of particular interest. Knockdown of DHX9 in ADAR1-dependent cell lines caused cell death and activation of the dsRNA sensor PKR. In ADAR1-independent cell lines, combined knockdown of DHX9 and ADAR1, but neither alone, caused activation of multiple dsRNA sensing pathways leading to a viral mimicry phenotype. Together, these results reveal an important role for DHX9 in suppressing dsRNA sensing by multiple pathways.

Triple-negative breast cancer (TNBC) remains a challenge to clinicians, laboratory investigators, and patients due to its disproportionate number of breast cancer deaths and its lack of an established therapeutic target. Numerous studies have identified potential novel mutational gene targets in TNBC, but single-agent therapeutics have lacked substantial impact in TNBC. Novel effective therapies are desperately needed. Alongside these therapies, we need accurate biomarkers that can be used to predict which patients will respond. We find that the ARF tumor suppressor expression is lost alongside p53 mutation in 60% of TNBC. ARF is the key player in sensing cellular oncogene-induced stress, such as signals emanating from oncogenic Ras and Myc alleles. ARF suppresses tumor formation in both p53-dependent and -independent mechanisms by interacting with proteins within the cell nucleolus. Our findings have advanced the premise that the p53-indendent functions of ARF are critical to preventing epithelial-based cancers. Our data show that mammary epithelial cells rapidly induce ARF expression in vitro and in vivo upon loss of functional p53. This induced ARF suppresses mammary tumor formation in vivo, wherein loss of both p53 and ARF dramatically accelerates tumorigenesis. This is consistent with our evidence that ARF and p53 function are concomitantly lost in TNBC. Potentially stemming from the dual loss of ARF and p53, we have observed that type I IFN signaling is elevated in TNBC. Our laboratory and others have shown that cancer cell lines, including those derived from TNBC, with elevated IFN signaling are dependent on the RNA deaminase ADAR1. Loss of ADAR1 in these cells leads to hyperactivation of the type I IFN pathway and cell death. We hypothesized that loss of ARF and p53 results in elevated type I IFN signaling and sensitizes cells to ADAR1 depletion. Beyond the potential genetic interaction between ARF-loss and ADAR1-dependency in TNBC, recent work from our lab has revealed that ARF and ADAR1 physically interact in cells lacking functional p53. We find that ARF can fully titrate much of the cellular ADAR1 into ARF complexes. Additionally, TNBC cells, but not non-TNBC cells, are sensitive to ADAR1 knockdown. Sensitivity to ADAR1 depletion appears to require type I IFN signaling and subsequent PKR activation. Analysis of primary human TNBC showed a marked separation of IFN signaling and ADAR1 localization/function between African American and Caucasian TNBC patients, suggesting that this pathway may serve as a functional marker of African American TNBC. Citation Format: Kyle Cottrell, Pat Kung, Sua Ryu, Leonard Maggi, Catherine Kuzmicki, Raleigh Kladney, Ling Yiu, Graham Colditz, Jason D. Weber. Reducing disparities in breast cancer mortality through the identification of novel targets in triple-negative breast cancer [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr IA012.

Research Overview and Objective Triple-negative breast cancer (TNBC) accounts for one-fifth of the breast cancer patient population. The heterogeneous nature of TNBC and lack of options for targeted therapy make its treatment a constant challenge. The co-deficiency of tumor suppressors p53 and ARF is a significant genetic signature enriched in TNBC, but it is not yet clear how TNBC is regulated by this genetic alteration. Methods To answer this question, we established p53/ARF-defective murine embryonic fibroblast (MEF) to study the molecular and phenotypic consequences in vitro. Moreover, transgenic mice were generated to investigate the effect of p53/ARF deficiency on mammary tumor development in vivo. Results Increased transformation capability was observed in p53/ARF-defective cells, and formation of aggressive mammary tumors was also seen in p53−/−ARF−/− mice. RNA-editing enzyme ADAR1 was identified as a potential mediator for the elevated oncogenic potential. Interestingly, we found that the overexpression of ADAR1 is also prevalent in human TNBC cell lines and patient specimen. Using short hairpin RNA (shRNA) to reduce ADAR1 expression abrogated the oncogenic potential of human TNBC cell lines, while non-TNBC cells are less susceptible. Different levels of RNA editing of known ADAR1 targets were detected in shRNA-treated human TNBC cell lines, suggesting that ADAR1-mediated RNA editing contributes to TNBC pathogenesis. Implication/Discussion These results indicate critical roles played by the tumor suppressors p53 and ARF in the pathogenesis of TNBC, partially through affecting ADAR1-mediated RNA editing. Further understanding of this pathway could shed light on potential vulnerabilities of TNBC and inform the development of personalized therapies based on patients’ genetic signiatures. Citation Format: Che-Pei Kung, Catherine E Kuzmicki, Emily A Bross, Sua Ryu, Eric Freeman, Thwisha Sabloak, Emily R Bramel, Leonard B Maggi Jr, Jason D Weber. Tumor suppressors p53 and ARF control ADAR1-driven tumorigenicity in triple negative breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-08-03.

Adenosine deaminase acting on RNA (ADAR) is an RNA-editing enzyme that binds dsRNA and converts adenosine to inosine. ADAR promotes cell survival and proliferation in multiple types of tumors, including breast cancer. However, the mechanism of ADAR-driven oncogenicity is not fully established. We focused on ADAR p110, the constitutively expressed and nuclear-localized isoform, and its role in managing genotoxic stress in cancer. ADAR p110 is involved in resolving R-loops, the DNA-RNA hybrids produced during transcription, and DNA damage response (DDR). We sought to elucidate the mechanism of ADAR-associated R-loop resolution and DDR that can be targeted in breast cancer. To identify ADAR-interacting proteins, proximity labeling was performed using ADAR p110 fused to ascorbate peroxidase (APEX2), followed by mass spectrometry. Among the positively enriched hits, known ADAR-interacting proteins associated with R-loop and DDR were validated by immunoprecipitation and immunofluorescence. DEAD-box helicase DDX54 was among the nine RNA helicases interacting with ADAR. DDX54 and ADAR showed an additive effect on preventing γH2AX signal. Additionally, knockdown (KD) of DDX54 increased ADAR expression, whereas ADAR KD did not affect DDX54 expression. These results suggest that DDX54 coordinates with ADAR to prevent genotoxic stress in breast cancer cells. As DDX54 and ADAR are both associated with R-loop resolution and DDR, we hypothesize that DDX54 and ADAR suppress R-loop accumulation and/or other types of genotoxic stress. This may be through independent pathways despite the physical interaction between ADAR and DDX54. Citation Format: Sua Ryu, Kyle A. Cottrell, Luisángely Soto-Torres, Angela Schabb, Jason D. Weber. ADAR and DDX54 promote genomic stability in breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 842.

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