Validation of a DNA Methylation Signature of Favorable Prognosis in Newly Diagnosed Acute Myeloid Leukemia.

Abstract 1615

Poster Board I-641

Epigenetic modifications are defined as heritable alterations in gene expression with no accompanying change in DNA sequence. Disruption of the epigenetic balance has major impact on chromatin structure and transcriptional activity. Hypermethylation of CpG islands within or near gene promoter regions is associated with gene silencing via transcriptional inactivation in human carcinogenesis. This gene silencing has the potential not only to affect disease progression, but also drug resistance and clinical outcome. We have previously reported that patients with Acute Myeloid Leukemia (AML) who are cured by conventional chemotherapy often display intense and simultaneous hypermethylation of multiple genes. To confirm these data, we evaluated the aberrant promoter methylation of these 9 genes in 68 patients with AML [excluding Acute Promyelocytic Leukemia, patients with inv-16 or t(8:21) and patients over the age of 65] enrolled on a clinical trial of conventional chemotherapy (idarubicin + cytarabine). Methylation at diagnosis was studied using bisulfite pyrosequencing. The patients had a median age of 52.5 years, median WBC count of 8,450/mm³, and the cytogenetic distribution was 3% favorable, 48% diploid and 49% poor-risk. Complete response rate was 71%. After a median follow-up of 24 months, median survival was 17 months, and median relapse-free survival 14 months. Dense methylation (>25% of CpG sites) was present in 7% of cases for HIN1; 12% for NOR1 and OLIG2; 15% for SLC26A4; 19% for NPM2 and P15INK4b; 24% for PGRA; 25% for CDH13 and 26% for PGRB genes. In univariate analyses, traditional factors like age, achievement of a complete remission, cytogenetics, history of myelodysplastic syndrome or myeloproliferative neoplasm, a sustained hematological response, and platelet count at diagnosis had their usual prognostic impact suggesting that this cohort is typical of the general AML population. Individually, dense methylation of each of NOR1, NPM2, HIN1, P15INK4b, SLC26A4, PGRA and PGRB genes was associated with a trend for improved overall survival, which was significant for PGRB (p=0.03) and near-significant for HIN1 (p=0.08) and NPM2 (p=0.1). A subgroup of 8 patients out of the 68 (11.8%) was strikingly distinct with 5 genes or more methylated in each case, and corresponded to a previously described CpG Island Methylator Phenotype (CIMP) in AML. These cases had similar age and cytogenetics as CIMP-negative cases. Median OS in CIMP-positive cases had not yet been reached at the time of analysis, compared to 15 months for CIMP-negative cases (p=0.03). The estimated 2-year survival rate was of 88% for CIMP-positive cases, compared to 40% for CIMP-negative cases (p=0.01). These results validate our previous findings of an association between increased DNA methylation and good prognosis in relatively young patients with AML who receive standard induction chemotherapy. The mechanism of this association between CIMP and survival is unknown, and we speculate that it relates to the inactivation of a gene that protects cells from the effects of chemotherapy. We conclude that epigenetic profiling using DNA methylation can help identify an AML patient subpopulation that may particularly benefit from conventional chemotherapy.