HOX expression patterns identify a common signature for favorable AML

Abstract

Deregulated HOX expression, by chromosomal translocations and myeloid-lymphoid leukemia (MLL) rearrangements, is causal in some types of leukemia. Using real-time reverse transcription-PCR, we examined the expression of 43 clustered HOX, polycomb, MLL and FLT3 genes in 119 newly diagnosed adult acute myeloid leukemias (AMLs) selected from all major cytogenetic groups. Downregulated HOX expression was a consistent feature of favorable AMLs and, among these cases, inv(16) cases had a distinct expression profile. Using a 17-gene predictor in 44 additional samples, we observed a 94.7% specificity for classifying favorable vs intermediate/unfavorable cytogenetic groups. Among other AMLs, HOX overexpression was associated with nucleophosmin (NPM) mutations and we also identified a phenotypically similar subset with wt-NPM. In many unfavorable and other intermediate cytogenetic AMLs, HOX levels resembled those in normal CD34+ cells, except that the homogeneity characteristic of normal samples was not present. We also observed that HOXA9 levels were significantly inversely correlated with survival and that BMI-1 was overexpressed in cases with 11q23 rearrangements, suggesting that p19(ARF) suppression may be involved in MLL-associated leukemia. These results underscore the close relationship between HOX expression patterns and certain forms of AML and emphasize the need to determine whether these differences play a role in the disease process.

Figure 1

Bootstrap-validated hierarchical clustering of samples. We applied bootstrap-validated unsupervised hierarchical clustering, using the expression of 43 genes to cluster 119 samples (excluding four NAM cytogenetics). Clustering used a distance metric based on the Pearson correlation coefficient and average linkage. We performed bootstrap validation by resampling genes from the data matrix with replacement and then repeating the clustering. We recorded for each pair of samples the percentage of times, in 500 bootstrap samples, that they were included as part of the same cluster (cutting the dendrogram each time to produce seven clusters). The percentage of times each pair of samples is clustered together is illustrated in the main part of the image, ranging from 0% (pure blue) to 100% (pure yellow). Dendrograms for hierarchical clustering by Pearson correlation with average linkage are shown on both edges. Color bars indicate sample type, which includes normal (NORMAL) CD34+ controls (black), favorable (FAV) cytogenetics (blue), intermediate (INTERM) cytogenetics (green) and unfavorable (UNFAV) cytogenetics (red). Individual patient numbers are indicated along the bottom.

Figure 2

Kaplan-Meier survival curve for HOXA9 gene expression grouped by its tertiles. Patients in the lowest tertile of expression have better survival than patients with moderate or high expression of HOXA9 (P = 0.073).