Comprehensive Analysis Of HOX Gene Expression and DNA Methylation From 189 Primary AMLs Demonstrates Canonical Patterns Associated With Hematopoietic Stem/Progenitors and Recurrent AML Mutations

HOX genes encode a family of homeodomain transcription factors with important roles in hematopoiesis. Expression of HOX genes is also a common feature of acute myeloid leukemia (AML), and functional studies have suggested that HOX-dependent pathways may contribute to leukemogenesis. Although HOX expression is known to correlate with specific AML mutations, the patterns of expression of all 39 HOX genes in primary AML samples, and their relationships with recurrent AML mutations, are incompletely understood. In addition, little is known about the influence of AML mutations on DNA methylation at the HOX loci, and the relationship between HOX gene expression and methylation in AML.

In this study, we carried out a combined analysis of gene expression data from microarray and RNA-sequencing platforms and genome-wide DNA array-based methylation from 189 primary AML samples that have been previously characterized by either whole-genome or whole exome sequencing. We also measured expression and methylation using the same platforms from normal bone marrow subsets, including CD34+ cells, promyelocytes, monocytes, neutrophils and lymphocytes, and obtained expression data from CD34+ hematopoietic precursors generated from in vitro differentiation of human embryonic stem cells.

Our analysis confirmed previous work on the general patterns of HOX expression in AML. The HOXA and HOXB genes showed variation both within each cluster and across the AMLs, although high level expression was restricted to a subset of these genes, including HOXA3, HOXA5, HOXA7, HOXA9, HOXA10, HOXB2-HOXB4, and HOXB6, as well as HOX cofactor MEIS1; HOXC and HOXD genes were minimally expressed in all of the samples. These observations were orthogonally validated by RNA-seq, and with a targeted Nanostring expression platform. Consistent with previous studies, MLL-positive AML samples (n=11) expressed only HOXA genes and MEIS1. AML samples with CBFB-MYH11 rearrangements (n=12) showed expression of only MEIS1, and HOXB2-HOXB4 at moderate levels; RUNX1-RUNX1T1 (n=7) and PML-RARA (n=19) samples did not detectably express any HOX genes. In AMLs with a normal karyotype (n=85), we observed two distinct patterns; one pattern displayed little or no HOX gene expression (7/85; 8%), and another displayed canonical expression of a specific subset of the HOXA and HOXB genes and MEIS1 (78/85; 92%) with similar relative HOX gene expression levels in all cases. Comparison of this pattern with normal bone marrow revealed the same HOX expression pattern in normal CD34+ cells; additional analysis showed that this pattern was confined to hematopoietic stem/progenitor cells, but was not seen in more mature cells, including other CD34+ subsets, promyelocytes, monocytes and neutrophils. We also measured HOX gene expression in CD34+ hematopoietic precursors generated from in vitro differentiation of human embryonic stem cells, which revealed expression of only MEIS1 and the canonical HOXB genes, suggesting that activation of these genes may represent the earliest events in the HOX pathway of hematopoietic development. Correlation of HOX expression with recurrent AML mutations by gene set enrichment analysis demonstrated a significant association with NPM1 (P<10-4) and DNMT3A (P<10-2) mutations, but not with other recurrent somatic mutations, including FLT3,IDH1/IDH2, and TET2. Methylation at the HOX loci demonstrated patterns that correlated with HOX expression, including hypomethylation at HOX promoters in samples with high expression. However, additional mutation-specific patterns were apparent. For example, NPM1-mutant AMLs demonstrated a distinct methylation pattern that included hypomethylation at the HOXB3 promoter, which was not shared with CBFB-MYH11 cases or other AMLs with HOXB3 expression.

In summary, our comprehensive analysis demonstrates canonical expression and methylation patterns at the HOX loci in AML. These patterns correspond to specific recurrent AML mutations, and the dominant pattern in most normal karyotype AMLs mimics the signature of hematopoietic stem cells. This supports previous observations of developmental regulation of HOX genes in hematopoiesis, and implies that this normal stem cell signature is “captured” in the majority of AMLs with normal karyotype. In addition, distinct methylation patterns at HOX loci suggest that multiple regulatory mechanisms are involved in HOX expression in AML.