Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Evaluating the therapeutic potential of ADAR1 inhibition for triple-negative breast cancer

Oncogene volume 40, pages 189–202 (2021)Cite this article

Subjects

A Correction to this article was published on 09 February 2021

This article has been updated

Abstract

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: ADAR1 is highly expressed in all breast cancer subtypes.
Fig. 2: ADAR1 is required for TNBC survival and proliferation.
Fig. 3: ADAR1 is required for TNBC transformation and tumorigenesis.
Fig. 4: PKR is overexpressed in TNBC and activated upon ADAR loss.
Fig. 5: ADAR1-dependent TNBCs exhibit elevated ISG expression and INFAR1 loss rescues ADAR1-knockdown phenotype.

Similar content being viewed by others

Data and code availability

CCLE RNA-seq count data (CCLE_RNAseq_genes_counts_20180929.gct.gz, CCLE_RNAseq_rsem_transcripts_tpm_20180929.txt.gz) were obtained from the Broad Institute Cancer Cell Line Encyclopedia and is available at https://portals.broadinstitute.org/ccle/data. Dependency data (D2_combined_gene_dep_scores.csv, Achilles_gene_effect.csv) were obtained from Broad Institute DepMap Portal and is available at https://depmap.org/portal/download/. TCGA breast cancer RNA-seq (illuminahiseq_rnaseqv2-RSEM_genes, illuminahiseq_rnaseqv2-RSEM_isoforms_normalized) and clinical data (Merge_Clinical) were obtained from the Broad Institute FireBrowse and are available at http://firebrowse.org/. All custom R scripts used in this study are available on GitHub (https://github.com/cottrellka/ADAR_TNBC). Lentiviral production and transduction; flow cytometric analysis of apoptosis; cell proliferation and focus formation assays; soft agar transformation assay; polysome profiling; immunohistochemistry. These experiments were performed as previously described, and further details can be found in the Supplementary Information [46, 51, 52].

Change history

References

  1. Ademuyiwa FO, Tao Y, Luo J, Weilbaecher K, Ma CX. Differences in the mutational landscape of triple-negative breast cancer in African Americans and Caucasians. Breast Cancer Res Treat. 2017;161:491–9.

    CAS  PubMed  Google Scholar 

  2. Waks AG, Winer EP. Breast cancer treatment: a review. JAMA. 2019;321:288–300.

    CAS  PubMed  Google Scholar 

  3. Garrido-Castro AC, Lin NU, Polyak K. Insights into molecular classifications of triple-negative breast cancer: improving patient selection for treatment. Cancer Discov. 2019;9:176–98.

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Perou CM. Molecular stratification of triple-negative breast cancers. Oncologist. 2011;16:61–70.

    PubMed  Google Scholar 

  5. Anders CK, Abramson V, Tan T, Dent R. The evolution of triple-negative breast cancer: from biology to novel therapeutics. Am Soc Clin Oncol Educ Book. 2016;35:34–42.

    PubMed  Google Scholar 

  6. Fumagalli D, Gacquer D, Rothe F, Lefort A, Libert F, Brown D, et al. Principles governing A-to-I RNA editing in the breast cancer transcriptome. Cell Rep. 2015;13:277–89.

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Han L, Diao L, Yu S, Xu X, Li J, Zhang R, et al. The genomic landscape and clinical relevance of A-to-I RNA editing in human cancers. Cancer Cell. 2015;28:515–28.

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Paz-Yaacov N, Bazak L, Buchumenski I, Porath HT, Danan-Gotthold M, Knisbacher BA, et al. Elevated RNA editing activity is a major contributor to transcriptomic diversity in tumors. Cell Rep. 2015;13:267–76.

    CAS  PubMed  Google Scholar 

  9. Peng X, Xu X, Wang Y, Hawke DH, Yu S, Han L, et al. A-to-I RNA editing contributes to proteomic diversity in cancer. Cancer Cell. 2018;33:817–28.e7.

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Anantharaman A, Gholamalamdari O, Khan A, Yoon JH, Jantsch MF, Hartner JC, et al. RNA-editing enzymes ADAR1 and ADAR2 coordinately regulate the editing and expression of Ctn RNA. FEBS Lett. 2017;591:2890–904.

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Gumireddy K, Li A, Kossenkov AV, Sakurai M, Yan J, Li Y, et al. The mRNA-edited form of GABRA3 suppresses GABRA3-mediated Akt activation and breast cancer metastasis. Nat Commun. 2016;7:10715.

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Binothman N, Hachim IY, Lebrun JJ, Ali S. CPSF6 is a clinically relevant breast cancer vulnerability target: role of CPSF6 in breast cancer. EBioMedicine. 2017;21:65–78.

    PubMed  PubMed Central  Google Scholar 

  13. Dave B, Gonzalez DD, Liu ZB, Li X, Wong H, Granados S, et al. Role of RPL39 in metaplastic breast cancer. J Natl Cancer Inst. 2017;109:djw292.

  14. Nakano M, Fukami T, Gotoh S, Nakajima M. A-to-I RNA editing up-regulates human dihydrofolate reductase in breast cancer. J Biol Chem. 2017;292:4873–84.

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Song IH, Kim YA, Heo SH, Park IA, Lee M, Bang WS, et al. ADAR1 expression is associated with tumour-infiltrating lymphocytes in triple-negative breast cancer. Tumour Biol. 2017;39:1010428317734816.

    PubMed  Google Scholar 

  16. Sagredo EA, Blanco A, Sagredo AI, Perez P, Sepulveda-Hermosilla G, Morales F, et al. ADAR1-mediated RNA-editing of 3'UTRs in breast cancer. Biol Res. 2018;51:36.

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Mannion NM, Greenwood SM, Young R, Cox S, Brindle J, Read D, et al. The RNA-editing enzyme ADAR1 controls innate immune responses to RNA. Cell Rep. 2014;9:1482–94.

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Liddicoat BJ, Piskol R, Chalk AM, Ramaswami G, Higuchi M, Hartner JC, et al. RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself. Science. 2015;349:1115–20.

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Pestal K, Funk CC, Snyder JM, Price ND, Treuting PM, Stetson DB. Isoforms of RNA-editing enzyme ADAR1 independently control nucleic acid sensor MDA5-Driven autoimmunity and multi-organ development. Immunity. 2015;43:933–44.

    CAS  PubMed  PubMed Central  Google Scholar 

  20. George CX, Ramaswami G, Li JB, Samuel CE. Editing of cellular Self-RNAs by adenosine deaminase ADAR1 suppresses innate immune stress responses. J Biol Chem. 2016;291:6158–68.

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Li Z, Okonski KM, Samuel CE. Adenosine deaminase acting on RNA 1 (ADAR1) suppresses the induction of interferon by measles virus. J Virol. 2012;86:3787–94.

    PubMed  PubMed Central  Google Scholar 

  22. Pujantell M, Riveira-Munoz E, Badia R, Castellvi M, Garcia-Vidal E, Sirera G, et al. RNA editing by ADAR1 regulates innate and antiviral immune functions in primary macrophages. Sci Rep. 2017;7:13339.

    PubMed  PubMed Central  Google Scholar 

  23. Gannon HS, Zou T, Kiessling MK, Gao GF, Cai D, Choi PS, et al. Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells. Nat Commun. 2018;9:5450.

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Liu H, Golji J, Brodeur LK, Chung FS, Chen JT, deBeaumont RS, et al. Tumor-derived IFN triggers chronic pathway agonism and sensitivity to ADAR loss. Nat Med. 2019;25:95–102.

    CAS  PubMed  Google Scholar 

  25. Chung H, Calis JJA, Wu X, Sun T, Yu Y, Sarbanes SL, et al. Human ADAR1 prevents endogenous RNA from triggering translational shutdown. Cell. 2018;172:811–24.e14.

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Lehmann BD, Jovanović B, Chen X, Estrada MV, Johnson KN, Shyr Y, et al. Refinement of triple-negative breast cancer molecular subtypes: implications for neoadjuvant chemotherapy selection. PLoS One. 2016;11:e0157368.

    PubMed  PubMed Central  Google Scholar 

  27. Ishizuka JJ, Manguso RT, Cheruiyot CK, Bi K, Panda A, Iracheta-Vellve A, et al. Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade. Nature. 2019;565:43–8.

    CAS  PubMed  Google Scholar 

  28. McFarland JM, Ho ZV, Kugener G, Dempster JM, Montgomery PG, Bryan JG, et al. Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. Nat Commun. 2018;9:4610.

    PubMed  PubMed Central  Google Scholar 

  29. Meyers RM, Bryan JG, McFarland JM, Weir BA, Sizemore AE, Xu H, et al. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nat Genet. 2017;49:1779–84.

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Wang Q, Miyakoda M, Yang W, Khillan J, Stachura DL, Weiss MJ, et al. Stress-induced apoptosis associated with null mutation of ADAR1 RNA editing deaminase gene. J Biol Chem. 2004;279:4952–61.

    CAS  PubMed  Google Scholar 

  31. Sakurai M, Shiromoto Y, Ota H, Song C, Kossenkov AV, Wickramasinghe J, et al. ADAR1 controls apoptosis of stressed cells by inhibiting Staufen1-mediated mRNA decay. Nat Struct Mol Biol. 2017;24:534–43.

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Chen L, Li Y, Lin CH, Chan TH, Chow RK, Song Y, et al. Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma. Nat Med. 2013;19:209–16.

    PubMed  PubMed Central  Google Scholar 

  33. Shigeyasu K, Okugawa Y, Toden S, Miyoshi J, Toiyama Y, Nagasaka T, et al. AZIN1 RNA editing confers cancer stemness and enhances oncogenic potential in colorectal cancer. JCI Insight. 2018;3:e99976.

    PubMed Central  Google Scholar 

  34. Crews LA, Jiang Q, Zipeto MA, Lazzari E, Court AC, Ali S, et al. An RNA editing fingerprint of cancer stem cell reprogramming. J Transl Med. 2015;13:52.

    PubMed  PubMed Central  Google Scholar 

  35. Li Y, Banerjee S, Goldstein SA, Dong B, Gaughan C, Rath S, et al. Ribonuclease L mediates the cell-lethal phenotype of double-stranded RNA editing enzyme ADAR1 deficiency in a human cell line. Elife. 2017;6:e25687.

  36. Dar AC, Dever TE, Sicheri F. Higher-order substrate recognition of eIF2alpha by the RNA-dependent protein kinase PKR. Cell. 2005;122:887–900.

    CAS  PubMed  Google Scholar 

  37. Sidrauski C, McGeachy AM, Ingolia NT, Walter P. The small molecule ISRIB reverses the effects of eIF2alpha phosphorylation on translation and stress granule assembly. Elife. 2015;4:e05033.

  38. Holcik M, Sonenberg N. Translational control in stress and apoptosis. Nat Rev Mol Cell Biol. 2005;6:318–27.

    CAS  PubMed  Google Scholar 

  39. Silverman RH, Skehel JJ, James TC, Wreschner DH, Kerr IM. rRNA cleavage as an index of ppp(A2'p)nA activity in interferon-treated encephalomyocarditis virus-infected cells. J Virol. 1983;46:1051–5.

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Holcik M. Could the eIF2alpha-independent translation be the Achilles heel of cancer? Front Oncol. 2015;5:264.

    PubMed  PubMed Central  Google Scholar 

  41. Kung CP, Maggi LB Jr., Weber JD. The role of RNA editing in cancer development and metabolic disorders. Front Endocrinol. 2018;9:762.

    Google Scholar 

  42. Doherty MR, Cheon H, Junk DJ, Vinayak S, Varadan V, Telli ML, et al. Interferon-beta represses cancer stem cell properties in triple-negative breast cancer. Proc Natl Acad Sci USA. 2017;114:13792–7.

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Doherty MR, Parvani JG, Tamagno I, Junk DJ, Bryson BL, Cheon HJ, et al. The opposing effects of interferon-beta and oncostatin-M as regulators of cancer stem cell plasticity in triple-negative breast cancer. Breast Cancer Res. 2019;21:54.

    PubMed  PubMed Central  Google Scholar 

  44. Lan Q, Peyvandi S, Duffey N, Huang YT, Barras D, Held W, et al. Type I interferon/IRF7 axis instigates chemotherapy-induced immunological dormancy in breast cancer. Oncogene. 2019;38:2814–29.

    CAS  PubMed  Google Scholar 

  45. Snell LM, McGaha TL, Brooks DG. Type I interferon in chronic virus infection and cancer. Trends Immunol. 2017;38:542–57.

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Forys JT, Kuzmicki CE, Saporita AJ, Winkeler CL, Maggi LB Jr., Weber JD. ARF and p53 coordinate tumor suppression of an oncogenic IFN-beta-STAT1-ISG15 signaling axis. Cell Rep. 2014;7:514–26.

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Lo PK, Yao Y, Lee JS, Zhang Y, Huang W, Kane MA, et al. LIPG signaling promotes tumor initiation and metastasis of human basal-like triple-negative breast cancer. Elife. 2018;7.

  48. Brenot A, Knolhoff BL, DeNardo DG, Longmore GD. SNAIL1 action in tumor cells influences macrophage polarization and metastasis in breast cancer through altered GM-CSF secretion. Oncogenesis. 2018;7:32.

    PubMed  PubMed Central  Google Scholar 

  49. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.

    CAS  PubMed  Google Scholar 

  50. Marcotte R, Sayad A, Brown KR, Sanchez-Garcia F, Reimand J, Haider M, et al. Functional genomic landscape of human breast cancer drivers, vulnerabilities, and resistance. Cell. 2016;164:293–309.

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Apicelli AJ, Maggi LB Jr., Hirbe AC, Miceli AP, Olanich ME, Schulte-Winkeler CL, et al. A non-tumor suppressor role for basal p19ARF in maintaining nucleolar structure and function. Mol Cell Biol. 2008;28:1068–80.

    CAS  PubMed  Google Scholar 

  52. Liu H, Dowdle JA, Khurshid S, Sullivan NJ, Bertos N, Rambani K, et al. Discovery of stromal regulatory networks that suppress Ras-sensitized epithelial cell proliferation. Dev Cell. 2017;41:392–407.e6.

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported by R01CA190986 (JDW), F32GM131514 (KAC), and TL1TR002344 (C-PK) from the National Institute of Health, and W81XWH-18-1-0025 from the Department of Defense (JDW). This work was supported by the Longer Life Foundation: A RGA/Washington University partnership. We thank Kazuko Nishikura (The Wistar Institute) for providing ADAR1 expressing constructs. The results shown here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.

Author information

Author notes

  1. These authors contributed equally: Che-Pei Kung, Kyle A. Cottrell

Authors and Affiliations

  1. Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, MO, USA

    Che-Pei Kung, Kyle A. Cottrell, Sua Ryu, Emily R. Bramel, Raleigh D. Kladney, Emily A. Bao, Eric C. Freeman, Thwisha Sabloak, Leonard Maggi Jr. & Jason D. Weber

  2. Department of Cell Biology and Physiology, Siteman Cancer Center, Washington University School of Medicine, Saint Louis, MO, USA

    Jason D. Weber

Authors
  1. Che-Pei Kung
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kyle A. Cottrell
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sua Ryu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Emily R. Bramel
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Raleigh D. Kladney
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Emily A. Bao
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Eric C. Freeman
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Thwisha Sabloak
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Leonard Maggi Jr.
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Jason D. Weber
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualization: C-PK, KAC, and JDW; methodology: C-PK, KAC, and JDW; software: KAC; investigation: C-PK, KAC, SR, ERB, RDK, EAB, ECF, TS, LM, and JDW; writing—original draft: C-PK and KAC; writing—review and editing: C-PK, KAC, SR, ERB, RDK, LM, and JDW; funding acquisition: JDW; supervision: JDW.

Corresponding author

Correspondence to Jason D. Weber.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

The original online version of this article was revised: The word “orthopedic” was changed to “orthotopic” in subheading “Mammary gland orthotopic implantation” and in the first sentence of section “Mammary gland orthotopic implantation”.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kung, CP., Cottrell, K.A., Ryu, S. et al. Evaluating the therapeutic potential of ADAR1 inhibition for triple-negative breast cancer. Oncogene 40, 189–202 (2021). https://doi.org/10.1038/s41388-020-01515-5

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41388-020-01515-5

This article is cited by

Search

Advanced search

Quick links