Hypomethylation of TET 2 Target Genes Identifies a Curable Subset of Acute Myeloid Leukemia

Background: Acute myeloid leukemia (AML) is curable in a subset of cases. The DNA methylation regulator TET2 is frequently mutated in AML, and we hypothesized that studying TET2-specific differentially methylated CpGs (tet2-DMCs) improves AML classification. Methods: We used bisulfite pyrosequencing to analyze the methylation status of four tet2-DMCs (SP140, MCCC1, EHMT1, and MTSS1) in a test group of 94 consecutive patients and a validation group of 92 consecutive patients treated with cytarabinebased chemotherapy. Data were analyzed with hierarchical clustering, Cox proportional hazards regression, and KaplanMeier analyses. All statistical tests were two-sided. Results: In the test cohort, hierarchical clustering analysis identified low levels of tet2-DMC methylation in 31 of 94 (33%) cases, and these had markedly longer overall survival (median survival 72+ vs 14 months, P = .002). Similar results were seen in the validation cohort. tet2-DMC–low status was shown to be an independent predictor of overall survival (hazard ratio = 0.29, P = .0002). In The Cancer Genome Atlas (TCGA) dataset where DNA methylation was analyzed by a different platform, tet2-DMC–low methylation was also associated with improved outcome (median survival = 55 vs 15 months, P = .0003) and was a better predictor of survival than mutations in TET2, IDH1, or IDH2, individually or combined. Conclusions: Low levels of tet2-DMC methylation define a subgroup of AML that is highly curable and cannot be identified solely by genetic and cytogenetic analyses. Acute myeloid leukemia (AML) is a highly heterogeneous hematologic malignancy. Most genetic and cytogenetic changes in AML have now been identified. Although these genetic changes are useful for classification and prognostication (1–3), they do not fully explain the clinical heterogeneity in outcomes. About half of patients with AML have an intermediate cytogenetic risk where heterogeneity remains problematic. Recent advances in the treatment for AML have improved outcomes for young patients through chemo-intensification and/or the use of allogeneic bone marrow transplantation (4). About half of young patients can be cured by chemotherapy alone, and identifying this curable subset will facilitate management of AML. Epigenetic mechanisms such as DNA methylation are important in control of gene expression in stem cell physiology, normal differentiation, and cancer development (5,6). DNA methylation is frequently abnormal in AML as examined by studies of individual genes and genome wide (7–10). DNA methylation patterns can also be prognostic in AML, either when studied genome-wide (11) or in a gene-specific manner (12,13). In addition, clinical studies with DNA methyltransferase inhibitors D ow naded rom http/academ ic.p.com /jnci/article-ab108/2/djv323/2457810 by gest on 31 M arch 2019 J. Yamazaki et al. | 2 of 9 a r t ic le a r t ic le have shown impressive responses in some patients (14), suggesting that aberrant DNA methylation may be a hallmark of the disease. Several genes encoding DNA methylation enzymes (DNMT3A) (15), DNA demethylating enzymes (TET2) (16), and related genes (IDH1/2) are mutated in AML (17). TET2 and IDH1/2 mutations are potentially important because animal models of these replicate aspects of the human phenotype (18,19). TET2, IDH1, and IDH2 mutations tend to be mutually exclusive and are thought to cause leukemia by inducing aberrant DNA methylation at specific targets (10). The prognostic impact of TET2, IDH1, and IDH2 status has been difficult to ascertain because of contradictory findings in different studies. For example, a bad outcome for TET2 mutations was seen in some studies (16,20,21), whereas no difference was seen in others (22,23). Similarly, IDH mutations were shown to be unfavorable in one study (IDH1) (24), favorable in one (IDH2) (25), and had no effect on survival in others (IDH2 and IDH1) (26,27). Because all three genes are thought to affect a common number of targets, we hypothesized that DNA methylation analysis of these targets may be more useful for prognostic purpose. We previously identified differentially methylated CpG sites in TET2-mutant cases of CMML (TET2-specific differentially methylated CpGs; tet2-DMCs) (28,29). Most of them were found to be outside CpG islands and have enrichment at hematopoietic-specific enhancers marked by H3K4me1 and at binding sites for the transcription factor p300. These tet2-DMCs have not previously been characterized in AML. In this study, we used bisulfite pyrosequencing to determine the DNA methylation status of four tet2-DMCs and found that low levels of methylation define a curable subset of AML that cannot be identified with cytogenetics and genetics alone.