Epigenetic reprogramming reverses the relapse-specific gene expression signature and restores chemosensitivity in childhood B-lymphoblastic leukemia

Abstract

Whereas the improvement in outcome for children with acute lymphoblastic leukemia has been gratifying, the poor outcome of patients who relapse warrants novel treatment approaches. Previously, we identified a characteristic relapse-specific gene expression and methylation signature associated with chemoresistance using a large cohort of matched-diagnosis relapse samples. We hypothesized that "reversing" such a signature might restore chemosensitivity. In the present study, we demonstrate that the histone deacetylase inhibitor vorinostat not only reprograms the aberrant gene expression profile of relapsed blasts by epigenetic mechanisms, but is also synergistic when applied before chemotherapy in primary patient samples and leukemia cell lines. Furthermore, incorporation of the DNA methyltransferase inhibitor decitabine led to reexpression of genes shown to be preferentially methylated and silenced at relapse. Combination pretreatment with vorinostat and decitabine resulted in even greater cytotoxicity compared with each agent individually with chemotherapy. Our results indicate that acquisition of chemoresistance at relapse may be driven in part by epigenetic mechanisms. Incorporation of these targeted epigenetic agents to the standard chemotherapy backbone is a promising approach to the treatment of relapsed pediatric acute lymphoblastic leukemia. IntroductionRelapsed acute lymphoblastic leukemia (ALL) is one of the leading causes of death among children with cancer. A hallmark of relapsed blasts is their intrinsic chemoresistance compared with what is observed at initial diagnosis. 1,2 Given the frequent failure of conventional salvage chemotherapy, including intensified drug schedules and stem cell transplantation, in the treatment of relapsed ALL, 3,4 innovative strategies are urgently needed.In recent years, it has become clear that cancer can be driven by patterns of altered gene expression mediated not by mechanisms that affect the primary DNA sequence, but through the "epigenetic" processes of DNA-promoter methylation and histone modification. 5,6 DNA methylation is catalyzed by DNA methyltransferases (DNMTs) and has been shown to be an important contributor to carcinogenesis, acting by silencing tumor suppressor genes in many tumor types, including hematologic malignancies. 6,7 Chromatin structure is also regulated by the "histone code," which refers to posttranslational modifications (ie, methylation, acetylation, phosphorylation, and ubiquitination) of key lysine residues on core histone proteins. 8 These 2 epigenetic processes of DNA-promoter methylation and histone modifications are clearly interdependent and coordinated. [9][10][11][12] DNMT inhibitors such as 5-azacitidine and decitabine have the potential to reverse promoter hypermethylation in tumor cells, leading to reexpression of aberrantly silenced genes and inducing tumor cell death. 13 DNMT inhibitors have been demonstrated to be effective therapy for myelodysplastic syndrome, which is characterized by global promoter hypermethylation. 14...

Entinostat Prevents Leukemia Maintenance in a Collaborating Oncogene-Dependent Model of Cytogenetically Normal Acute Myeloid Leukemia

“…Entinostat prolonged survival in leukemic mice as a single-agent to a similar level as that reported for continuous infusion of a potent small molecule inhibitor [44]. However, epigenetic priming agents, such as HDACis and hypomethylating molecules will most likely be more effective as part of a combined therapeutic approach in leukemia and cancer [45][46][47]. HDACis are associated with several modes of antitumor activity including modulation of the immune response [48], cell cycle arrest, promotion of differentiation, senescence, and apoptosis [46].…”

Epigenetic control of epithelial-mesenchymal-transition in human cancer

“…With respect to basic cell culture experiments showing the influence of epigenetics on therapy responsiveness or resistance (101), recent data demonstrate that the epigenetic pre-treatment of human cancer cells induces differentiation and, therefore, presents us with a chance to improve the efficiency of classical chemotherapies (102). Therefore, we hypothesize that epigenetic therapy may stabilize the epithelial tumor phenotype or induce MET which may subsequently improve tumor sensitivity to conventional chemotherapy (Fig.…”

Loss of TBL1XR1 Disrupts Glucocorticoid Receptor Recruitment to Chromatin and Results in Glucocorticoid Resistance in a B-Lymphoblastic Leukemia Model

“…A lower concentration of prednisolone was used in this experiment to avoid high levels of cell death associated with treating SAHA-pretreated cells with higher doses of prednisolone. It is not surprising that treatment with SAHA leads to decreased cell viability because SAHA has previously been shown to be toxic to leukemic cells (30,36); however, the restoration of GILZ induction in the TBL1XR1 knockdown cells does suggest that the impact of SAHA is mediated in part by the rescue of glucocorticoid signaling. These results are in agreement with the NCoR1 depletion studies showing the pivotal role of NCoR1 (and its associated HDACs) in mediating the GC resistance associated with loss of TBL1XR1.…”

“…RS4;11 and UOCB1 cells have also been previously used to characterize pathways that mediate prednisolone sensitivity (27,28). It should be noted that although Reh cells have been characterized as having undetectable levels of GR (29), we have previously shown that Reh cells respond to steroid treatment comparably to primary patient samples, as well as other ALL cell lines, and express GR (30). We authenticated our parental Reh cell lines through short tandem repeat analysis by ATCC, and cytogenetic analysis confirmed the t(12;21), EVT6/RUNX1 translocation by cytogenetic analysis (data not shown).…”

“…Importantly, pretreatment with an HDAC inhibitor reestablished GILZ transcriptional expression by prednisolone and reinstated chemosensitivity to prednisolone in cells depleted of TBL1XR1. Previous studies have also shown that chemosensitivity can be enhanced by pretreatment with epigenetic modifiers, and a clinical trial of SAHA (clinical trial NCT01483690) and decitabine combination therapy together with a backbone of conventional therapy is underway to directly assess the therapeutic potential of this approach in relapsed ALL (30,36).…”