DNA methyltransferase expression in triple-negative breast cancer predicts sensitivity to decitabine
Jia Yu, Bo Qin, Ann M. Moyer, Somaira Nowsheen, Tongzheng Liu, Sisi Qin, Yongxian Zhuang, Duan Liu, Shijia W. Lu, Krishna R. Kalari, Daniel W. Visscher, John A. Copland, Sarah A. McLaughlin, Alvaro Moreno-Aspitia, Donald W. Northfelt, Richard J. Gray, Zhenkun Lou, Vera J. Suman, Richard Weinshilboum, Judy C. Boughey, Matthew P. Goetz, Liewei Wang
Jia Yu, Bo Qin, Ann M. Moyer, Somaira Nowsheen, Tongzheng Liu, Sisi Qin, Yongxian Zhuang, Duan Liu, Shijia W. Lu, Krishna R. Kalari, Daniel W. Visscher, John A. Copland, Sarah A. McLaughlin, Alvaro Moreno-Aspitia, Donald W. Northfelt, Richard J. Gray, Zhenkun Lou, Vera J. Suman, Richard Weinshilboum, Judy C. Boughey, Matthew P. Goetz, Liewei Wang
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Research Article Oncology

DNA methyltransferase expression in triple-negative breast cancer predicts sensitivity to decitabine

Abstract

Triple-negative breast cancer (TNBC) is a heterogeneous disease with poor prognosis that lacks targeted therapies, especially in patients with chemotherapy-resistant disease. Since DNA methylation-induced silencing of tumor suppressors is common in cancer, reversal of promoter DNA hypermethylation by 5-aza-2′-deoxycytidine (decitabine), an FDA-approved DNA methyltransferase (DNMT) inhibitor, has proven effective in treating hematological neoplasms. However, its antitumor effect varies in solid tumors, stressing the importance of identifying biomarkers predictive of therapeutic response. Here, we focused on the identification of biomarkers to select decitabine-sensitive TNBC through increasing our understanding of the mechanism of decitabine action. We showed that protein levels of DNMTs correlated with response to decitabine in patient-derived xenograft (PDX) organoids originating from chemotherapy-sensitive and -resistant TNBCs, suggesting DNMT levels as potential biomarkers of response. Furthermore, all 3 methytransferases, DNMT1, DNMT3A, and DNMT3B, were degraded following low-concentration, long-term decitabine treatment both in vitro and in vivo. The DNMT proteins could be ubiquitinated by the E3 ligase, TNF receptor–associated factor 6 (TRAF6), leading to lysosome-dependent protein degradation. Depletion of TRAF6 blocked decitabine-induced DNMT degradation, conferring resistance to decitabine. Our study suggests a potential mechanism of regulating DNMT protein degradation and DNMT levels as response biomarkers for DNMT inhibitors in TNBCs.

Authors

Jia Yu, Bo Qin, Ann M. Moyer, Somaira Nowsheen, Tongzheng Liu, Sisi Qin, Yongxian Zhuang, Duan Liu, Shijia W. Lu, Krishna R. Kalari, Daniel W. Visscher, John A. Copland, Sarah A. McLaughlin, Alvaro Moreno-Aspitia, Donald W. Northfelt, Richard J. Gray, Zhenkun Lou, Vera J. Suman, Richard Weinshilboum, Judy C. Boughey, Matthew P. Goetz, Liewei Wang

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Figure 1

Protein levels of DNMTs correlated with decitabine sensitivity in a collection of breast cancer PDX–derived organoids.

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Protein levels of DNMTs correlated with decitabine sensitivity in a coll...
(A) Schematic representation of the work flow for generating organoid culture from TNBC PDX tumors. (B) Representative figures of organoid cultures derived from TNBC PDX tumor (MCD-02, resistant to decitabine treatment). Organoids were treated with 0 nM, 100 nM, 500 nM, or 1000 nM decitabine for 7 days and recovered for 2 days (n = 3 independent experiments). Scale bars: 20 μm. (C) Quantification of tumorsphere in B. Data represent mean ± SEM of control from n = 3 independent experiments. ***P < 0.001, 2-tailed t tests. (D) Organoids from 15 different TNBC PDX tumors were cultured and tested for decitabine sensitivity at a concentration of 100 nM for 7 days, followed by 2 days of recovery. Colors represent the degree of decitabine sensitivity. Red or orange indicates decitabine resistant; green indicates decitabine sensitive. Data represent mean ± SEM of n = 3 independent experiments when compared with control. (E) Protein levels of DNMT1, DNMT3A, and DNMT3B detected in the cell lysates isolated from untreated organoids. (F) Protein level correlation with organoid percentage of survival after decitabine treatment. The y axis represents the relative quantification of protein levels and the x axis represents the percentage of survival after 100 nM decitabine as in D.