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.

Treatment of human cells with 5-aza-dC induces formation of PARP1-DNA covalent adducts at genomic regions targeted by DNMT1

“…This antibody detected a modest increase in 89 kD PARP1 levels by 48 hr of 5-aza-dC treatment in K562 cells, and clearly increased levels in K562 cells treated with 5-aza-dC for 66 hr, and GM639 cells treated with 5-aza-dC followed by PARPi. DNMT1 levels were dramatically reduced upon 5-aza-dC treatment, as also documented in other cell types (Ghoshal et al, 2005;Yu et al, 2018). Surprisingly in K562 but not GM639 cells, DNMT1 levels began to recover at 66 hr; and treatment with PARPi alone or together with 5-aza-dC caused DNMT1 levels to increase.…”

“…5-aza-dC is incorporated into DNA of replicating cells, where it may become a target for methylation by the maintenance DNA methyltransferase, DNMT1. Treatment with 5-aza-dC rapidly induces proteolysis and depletion of DNMT1, resulting in genome-wide loss of cytosine methylation and extensive epigenetic reprogramming (Ghoshal et al, 2005;Patel et al, 2010;Yu et al, 2018). The possibility that DNA demethylation might re-activate silenced tumor suppressor genes to limit cell proliferation provided the initial rationale for the use of 5-aza-dC in therapy of cancer, and 5-aza-dC is 2 commonly considered an "epigenetic" drug (Estey, 2013).…”

miR‐155 increases stemness and decitabine resistance in triple‐negative breast cancer cells by inhibiting TSPAN5

“…Our previous studies showed that miR‐155 is upregulated in TNBC, but whether miR‐155 is involved in stemness and DCA resistance in BC has not been studied. Studies have shown that DNMT expression in TNBC is associated with sensitivity to DCA 33 . Studies have also shown that miR‐155 is a novel marker of TNBC chemoresistance 15 .…”

“…Studies have shown that DNMT expression in TNBC is associated with sensitivity to DCA. 33 Studies have also shown that miR-155 is a novel marker of TNBC chemoresistance. 15 Our findings support the notion that miR-155 promotes the stem cell characteristics, the colony-forming ability, and the DCA resistance of TNBC cells.…”

Precision medicine, agriculture, and genome editing: science and ethics

“…If residual tumor remained after chemotherapy was complete, another sample of tumor tissue was collected during surgical resection for derivation of a treatment‐resistant PDX. In the PDX model, a relationship between DNA methyltransferase ( DNMT ) expression and response to decitabine was observed, where PDXs with high expression of DNMT3A and DNMT3B exhibit an enhanced response to decitabine, suggesting that decitabine may be an alternative therapy for certain individuals. Such targeted therapies, based on individual tumor somatic genotypes using pharmacogenomic approaches, will yield additional therapeutic targets in the near future to further precision oncogenic strategies.…”