Allele-specific expression of GATA2 due to epigenetic dysregulation in CEBPA double mutated acute myeloid leukemia
Transcriptional deregulation is a central event in the development of acute myeloid leukemia (AML). Genetic variation in cis-regulatory regions usually involves a single allele, which results in differential expression of the two alleles. This phenomenon, termed allele-specific expression (ASE), is therefore an accurate marker for cis-regulatory variation. We proposed that a systematic study of genes with aberrant ASE in AML may uncover aberrantly expressed genes caused by abnormalities in cis-regulatory elements.
We performed whole exome sequencing (WES) and RNA-seq on leukemic blasts from 209 AML patients, representing all major subtypes of the disease. Combining both datasets, we assessed ASE in every gene with informative (non-homozygous) single nucleotide variants (SNVs). Moreover, we conducted ChIP-seq, ATAC-seq and bisulfite sequencing to investigate epigenetic changes in regions of interest.
The gene encoding GATA binding protein 2 (GATA2) displayed ASE more often than any other myeloid or cancer-related gene. GATA2 ASE was strongly associated with CEBPA double mutations (CEBPA DM), with 95% of cases presenting GATA2 ASE. CEBPA DM is a subtype with favorable clinical outcome which frequently co-occurs with GATA2 mutations, pointing to a functional connection between these two genes. Interestingly, CEBPA DM AML patients with GATA2 mutations preferentially expressed the mutated GATA2 allele. These findings were validated in the TCGA and Beat AML datasets, where all CEBPA DM patients with informative SNVs exhibited GATA2 ASE.
Using matched diagnostics-remission samples, we found that GATA2 ASE is a somatic event lost in complete remission, supporting the notion that it plays a role in CEBPA DM AML. Bisulfite sequencing data showed that acquisition of GATA2 ASE involved silencing of one allele via promoter methylation. Notably, promoter methylation was also lost in remission together with GATA2 ASE. However, expression levels were compensated by overactivation of the other allele, as shown by increased levels of H3K327ac ChIP-seq and eRNA.
In summary, GATA2 ASE is a somatic event that is epigenetically acquired in almost all CEBPA DM AML cases, suggesting it plays a key role in the development and/or progression of this leukemia subtype. The specific mechanisms remain unclear, but the importance of fine-tuned GATA2 regulation points to altered GATA2 levels. Thus, we propose that reduced levels of GATA2 mediated by allele-specific silencing, in collaboration with CEBPA mutations, might be an early event in leukemic transformation. Later compensation by over-activation of the super-enhancer would then result in stabilization of GATA2 levels in leukemic blasts.