A H3K9me3 chromatin signature predicts EFS in AML patients. (A) EFS analyses were performed according to Bair and Tibshirani.17 A predictor was built based on 91 genomic regions with significant association (P < .001) with EFS in 57 AML patients. Overall, 35 patients were predicted to be at high risk and 22 to be at low risk. The predictor separated well between patients with good and poor prognosis. Mean EFS was 43.5 months (low risk) versus 12.4 months (high risk). A permutation test analysis identified the quality of the predictor to be based on chance to be less than 10% (P = .07, permutation test). (B) A clinical predictor for EFS was built based on karyotype, age, and FLT3/NPM1 mutation status, which are the strongest clinical predictors for survival in AML patients. For this predictor, 26 and 31 patients were predicted to be at high and low risk, respectively. As expected, this predictor also separated well between surviving and nonsurviving patients. Mean EFS was 42.2 versus 17.5 months. (C) A combined predictor was built from H3K9me3 and the clinical covariates. For this predictor, 39 and 18 patients were predicted to be at high and low risk, respectively. This predictor predicted the outcome better than the clinical predictor (P = .02, permutation test). The EFS times of the predicted groups were 53.9 versus 17.2 months for the low-risk and the high-risk groups, respectively. (D) A heatmap of genomic loci whose H3K9me3 level were associated with EFS. The columns represent patient specimens that were ordered from the left to the right according to their EFS status and the time of censoring or event. Patients marked with the blue bar “Event Free Survival” were alive without relapse at the time of analysis. The bar in red indicates patients with relapse, refractory disease, or death. These were arranged with the longest EFS time on the left. Gene loci in rows were hierarchically clustered for H3K9me3 levels (red indicates low-level H3K9me3; and green, high-level H3K9me3). Two large clusters are visible with the group of good prognosis H3K9me3 patterns extending to 6 additional patients in the other group. *Each of these patients experienced an event more than 3 years after initial diagnosis indicating a generally more favorable prognosis. (E) Gene Ontology analysis of genes whose level of H3K9 trimethylation was closely associated with patient survival in the combined predictor. Indicated are Gene Ontology categories with at least 2.5-fold overrepresentation. All changes were statistically significant with P < .01.
