Epigenome profiling reveals aberrant DNA methylation signature in GATA2 deficiency.

Topic: 10. Myelodysplastic syndromes - Clinical Background: GATA2 deficiency is a complex multi-system disorder with high risk of developing myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) with a nearly complete lifetime penetrance. GATA2 carriers within families show variable expressivity and heterogeneity in clinical features with manifestation of myeloid neoplasm at any age. This suggests that both cooperating genetic and environmental drivers shape the course of the disease. Aims: We applied NGS and bead-array techniques to identify acquired somatic mutations and aberrant DNA methylation patterns in 20 Spanish GATA2 carriers, including 16 patients and 4 asymptomatic carriers. Methods: To identify acquired somatic mutations, we performed NGS of total PB and BM samples in 17 of the 20 GATA2 carriers. Then, using the Infinium Human Methylation EPIC 850 K platform (Illumina), we profiled DNA of 8 BM and 8 PB samples and compared with a cohort of 12 age-matched healthy donor (HD) controls. Results: Median age at the diagnosis was 36 (6–75) years. The primary initial manifestation was MDS (n=12, 55%), followed by immunodeficiency (n=3, 15%), and AML (n=2, 10%). On cytogenetics, trisomy 8 was detected in 3 patients, complex karyotype in 2 patients, while 11 patients had normal karyotype. Somatic mutations in myeloid malignancy genes were identified in 71% (12/17) tested patients. This analysis confirmed the heterogeneity of acquired somatic mutations in GATA2 deficiency, with STAG2, ASXL1 and SETBP1 as recurrently affected genes. Furthermore, an unbiased genome-wide screen for aberrant CpG island methylation revealed a specific hypermethylated pattern in GATA2 patients when compared with HD. In detail, 2834 differentially methylated positions (DMPs) were identified in GATA2-mutant BM samples and 1406 DMPs in PB samples. revealed that the majority of DMPs are promoter-distant in both, BM (Open Sea: 60% hypomethylated DMPs and 72.5% hypermethylated DMPs) and PB samples (Open Sea: 52% hypomethylated and 82.3% hypermethylated). Overall, we observed that DNA methylation changes are enriched in gene-distant and intronic regions in GATA2 patients. Interestingly, we identified the presence of a hypermethylated DMP subcluster across all the GATA2 patients, including the asymptomatic youngest asymptomatic one (6-years old). Importantly, the 2-year longitudinal follow-up of this patients showed the evolution to MDS with multilineage dysplasia (MDS-MLD) and monosomy 7 without secondary mutations. In contrast, the other asymptomatic GATA2 carriers with not apparent symptoms had DNA methylation profile comparable with the HD group. This observation suggests the presence of a likely early aberrant DNA methylation at specific loci in GATA2 carriers that might have a potential prognostic utility in early identifying patients at risk for impending myeloid transformation. Furthermore, Hypergeometric Optimization of Motif EnRichment (HOMER) analysis revealed in the hypermethylated DMPs a significant enrichment in TFs motives of the ETS family, which are known to play a role in MDS. Finally, integration of hypermethylated genes with a GATA2 ChIPseq dataset revealed that GATA2 deficiency is associated with aberrant DNA methylation in GATA2 target genes. Summary/Conclusion: We identified an aberrant DNA hypermethylated signature in GATA2 deficiency. Specifically, we described the presence of a subset of aberrant hypermethylated set of genes present in GATA2 carriers at early disease stage, which could be potentially used as predictors of clonal evolution. Keywords: GATA-2, Genetic, MDS/AML, Epigenetic