Why methylation is not a marker predictive of response to hypomethylating agents

Abstract

The azanucleotides azacitidine and decitabine have been shown to induce hematologic response and prolong survival in higher-risk myelodysplastic syndromes. They are inhibitors of DNA methyltransferase-1 and induce DNAhypomethylation. Induction of apoptosis is also clinically relevant, in particular during the first treatment cycles, when cytopenia is a frequent side-effect. Since the hypomethylating effect is reversible, and the malignant clone has been shown to persist in most responding patients, several cycles are necessary to achieve and maintain responses, while treatment interruption is associated with rapid relapse. Methylation studies have shown global and gene-specific hypermethylation in myelodysplastic syndromes, but there seems to be little relation between the degree of demethylation following hypomethylating treatment and hematologic response. The presence of concurrent genomic hypermethylation and hypomethylation may impair the predictive power of current detection techniques. This scenario has been complicated by the identification of epigenetic enzyme mutations, including TET2, IDH1/2, DNMT3A and EZH2, which are important for response to hypomethylating treatment. Changes in azanucleotide metabolism genes may also play a role. In the future, methylation analysis concentrating not only on promoters, but also on gene bodies and intergenic regions, may identify key genes in patients with the highest probability of response to azanucleotides and allow a patient-tailored approach. ABSTRACT © F e r r a t a S t o r t i F o u n d a t i o nmore mutated clones during the course of the disease, which were not influenced by the type of treatment. Loss of response after stopping treatment is further favored by the fact that leukemic stem cells included in the Lin-CD34 + compartment seem to be spared from the activity of the drugs, probably also due to their non-proliferating status. In 15 MDS and AML patients achieving complete remission following AZA and valproic acid treatment, Craddock et al. showed that leukemic stem cells were substantially reduced, but were never eradicated, and expansion of this population took place before morphological relapse.14 Leukemic stem cells have been shown to overexpress multidrug resistance (MDR) transporters, including P-glycoprotein (P-gp). 15 Hypomethylating drugs have been shown to down-regulate P-gp expression in myeloid cell lines, with decitabine demethylating the repressor binding site of the MDR-1 gene. [16][17] Higher-risk MDS are characterized by a high degree of global methylation compared to normal CD34 + cells and de novo acute myeloid leukemia (AML). 18,19 In MDS, different methods have been used to study global methylation. Some of them, including liquid chromatography-mass spectroscopy/mass spectroscopy (LC-MS/MS), capture of methylated DNA by methyl-binding protein (MBD2), and the LINE-1 and the LUMA assays, evaluate genomic methylation without distinguishing regulatory from structural regions. After the seminal studies in which specific gene promoters we...

Genome sequencing in myelodysplastic syndromes: can molecular mutations predict benefit from hypomethylating agent therapy?

“…After the disappointment of methylation predictive studies, the recent discoveries of >40 genes with recurrent somatic mutations in the vast majority of patients have renewed hope of identifying that evasive biomarker(s) [7,8,10]. The recurrent mutations were observed most commonly in genes involved in important biologic pathways that contribute to the pathogenesis of MDS such as DNA methylation (DNMT3A, TET2, IDH1 and IDH2), chromatin modification (EZH2 and ASXL1), transcriptional regulation (TP53, RUNX1 and GATA2), RNA splicing (SF3B1, U2AF1, SRSF2 and ZRSR2) and signal transduction (JAK2, KRAS and CBL) [14]. Several of these mutations were found to have an independent prognostic value and, interestingly, there appears to be no significant difference in survival impact of a specific mutation if present in a dominant clone versus a subclone [8].…”

Molecular Testing in Myelodysplastic Syndromes for the Practicing Oncologist: Will the Progress Fulfill the Promise?

“…Similarly, although the prognostic impact of IDH mutations in MDS is less clear, testing for these mutations should be considered as evidence suggesting they are important in pathogenesis of IDH-mutant myeloid malignancies, and their inhibitors have also entered early clinical trials [83][84][85]. In addition to molecular mutations, other predictive biomarkers (e.g., methylation signatures, UCK1 enzyme expression) are also under investigation [86][87][88][89]. Nonetheless, logistical issues related to assay performance standardization, validation, interpretation, and development of guidelines for how to use the results to inform clinical decisions are yet to be resolved [88][89][90][91].…”

MTHFR, TS and XRCC1 genetic variants may affect survival in patients with myelodysplastic syndromes treated with supportive care or azacitidine

“…27 However, recent studies reported that there is little relation between the degree of demethylation following hypomethylating treatment and hematologic response in patients with MDS. 28 In other words, methylation is not a predictive marker of response to hypomethylating agents for MDS patients, and therefore we cannot decide which patient can be a good candidate to receive these drugs taking only in account the degree of methylation. In this view, polymorphism in key genes regulating not only the metabolism of the cell, but also its sensitivity to certain type of drug, MDS specific, could represent a novel predictive marker that surely warrants further studies.…”