High Frequency of GATA2 Mutations in Cytogenetically Normal Acute Myeloid Leukemia with Biallelic CEBPA Mutations Identified by Exome Sequencing

Abstract 72

Cytogenetically normal acute myeloid leukemia (CN-AML) with biallelic CEBPA gene mutations (biCEPBA) represents a distinct genetic entity associated with a favorable clinical outcome (Dufour et al, JCO, 2010; Green et al, JCO, 2010; Pabst et al, Br J Cancer, 2009; Wouters et al, Blood, 2009). Furthermore, biCEBPA mutations are seldomly associated with other known prognostic mutations, like mutated NPM1 or FLT3-ITD. So far, it is not known if other alterations cooperate with the biCEBPA mutations in the process of leukemogenesis.

To identify collaborating mutations, we performed whole exome sequencing in five biCEBPA mutated CN-AML patients. We generated at least 5 Gbp of exome sequence for each of the biCEBPA AML samples and for the corresponding remission samples. This allowed us to cover at least 80% of RefSeq coding exon positions with a minimum read depth of 10. Comparison of the AML exome sequence with the remission exome sequence and exclusion of annotated polymorphisms led to the identification of leukemia-specific variants. So far, we were able to confirm between 2 to 10 non-synonymous coding somatic mutations per patient in addition to the previously known biCEBPA mutations using Sanger sequencing. Thus, we detected tumor-specific mutations (nonsense and missense) in a total of 22 genes. Two genes were found recurrently mutated in 2 of the 5 biCEBPA samples: DNMT3A (2/5) and GATA2 (2/5).

GATA2 is a zinc finger transcription factor important for haematopoietic stem cell proliferation and normal megakaryocytic development. GATA2 mutations have recently been associated with familial monocytopenia and familial myelodysplastic syndrome (Hsu et al, Blood, 2011; Scott et al, ASH abstract 2010). In the M5 subtype of AML, GATA2 mutations were found at a low frequency of 3.6% (Yan et al, Nature Genetics, 2011). Interestingly, GATA2 is a direct protein interactor and negative regulator of CEBPA. (Huang et al., MCB, 2009; Tong et al, MCB, 2005).

Therefore, we determined the frequency of GATA2 mutations in 32 patients with biCEBPA mutant AML by screening all coding exons of GATA2 using high resolution melting curve analysis. Aberrant melting curves were subsequently confirmed by Sanger sequencing. Interestingly, 13 out of 32 (40.6%) biCEBPA patients carried heterozygous missense mutations in GATA2 and strikingly these mutations were all located in the highly conserved N-terminal zinc finger domain of GATA2. The missense mutations A318T and G320D surrounding the C319 which coordiates the zinc atom were recurrently detected in 6 out of 13 biCEBPA patients (3 with A318T and 3 with G320D). Two patients were found to carry each two different mutations in GATA2. 4 out of 13 biCEBPA patients with GATA2 mutations who could be analyzed during molecular remission had lost the GATA2 mutation at remisssion. Furthermore, no GATA2 mutations were found in 38 patients with a monoallelic CEBPA mutation and in 90 CN-AML patients with wildtype CEBPA. We are currently analyzing the functional consequences of these GATA2 mutations.

In summary, we describe for the first time the specific association of mutations within the N-terminal zinc finger of GATA2 with biallelic CEBPA mutations in cytogenetically normal AML. Although high throughput sequencing so far has mainly revealed an increasing genetic heterogeneity in AML, our results suggest that there is an association of distinct mutations in defined genetic subgroups of AML.