H3K27me3 Level of the HIST1 Cluster Defines an Epigenetic Marker of Acute Myeloid Leukemia with Prognostic Value

Acute myeloid leukemia (AML) is the most common acute leukemia diagnosed in adults, characterized by significant heterogeneity in terms of biology and clinical outcome. Improvements in sequencing technologies have led to the discovery of frequent somatic mutations in epigenetic modifiers, placing epigenetic deregulation in the center of AML. Yet, the global view and the impact of this deregulation on disease characteristics are under investigation.

To gain a more comprehensive understanding of epigenetic deregulation in AML, particularly the heterogeneous subset with normal karyotype (CN-AML), associated with intermediate clinical prognosis, we performed H3K27me3 profiling on CN-AML patient samples. Primary bone marrow or peripheral blood samples containing more than 80% of blasts were selected from the Institut Paoli-Calmettes Biological Resources Center inventory for the purpose of genetic and epigenetic studies. We initially analyzed 35 CN-AML samples by ChIP coupled with hybridization on oligonucleotide promoter arrays (Chip-chip) for genomic H3K27me3 distribution. Clustering analysis revealed 586 highly H3K27me3-variable genomic regions across patients corresponding to 461 genes mostly involved in chromatin organization. The heterogeneity in the H3K27me3 profile was characterized by a remarkable H3K27me3 enrichment at the chromosome 6 p22.2-22 region that encompasses 70 kbp within the major HIST1 cluster. This striking H3K27me3 enrichment was covering 11 histone genes and was partially overlapping with the focal deletion at 6p22 found in acute lymphoblastic leukemia.

The HIST1 H3K27me3 enrichment profile clearly distinguished 2 groups of CN-AML patients based on their HIST1 H3K27me3 level. In order to independently extend this observation, we analyzed the H3K27me3 status by using ChIP followed by qPCR (ChIP-qPCR) at the same HIST1 genomic locations, in an independent cohort of 51 CN-AML patients. This revealed the presence of this abnormal epigenetic profile in about 50% of the patients.

CN-AML samples were split in two groups, according to the median H3K27me3 enrichment levels at the HIST1 cluster genes. These two groups were analyzed for clinical and molecular characteristics. Patients with high HIST1 H3K27me3 level had a markedly higher incidence of NPM1 mutation (89% vs. 40%; p= 1.75x10^-5) and a lower incidence of WT1 mutation (0% vs. 20%; p=0.028). No significant association was observed with FLT3 (ITD and TKD), IDH1/2, DNMT3A nor ASXL1 mutations. Patients with high HIST1 H3K27me3 level had a significant longer leukemia free survival at 5 years (allo-grafted patients censored, LFS-allo; 13.33 vs. 8.92 months p=0.0053). Moreover, multivariate analysis showed that HIST1 H3K27me3 status provided a more powerful prognostic indicator than the NPM1mut/FLT3-ITDneg and NPM1/FLT3-ITD genotypes.

In conclusion,using epigenetic profiling, our analysis has enabled the discovery of a new epigenetic alteration that affects CN-AML and impacts prognosis. We demonstrate that the HIST1 cluster is targeted by epigenetic events that lead to high H3K27me3 level and predicts a good prognosis. This may help refine risk stratification in AML, identifying a further group of patients unlikely to benefit from allogeneic transplantation in first remission. Overall, our data provide a proof of concept that epigenetic profiling could be used to discover new biomarkers with prognostic value.