Human iPSC-based modeling unveils chromatin remodeling induced by SETBP1 mutation as a potential initiating factor in GATA2 deficiency.

GATA2 deficient patients are prone to develop myelodysplastic syndrome (MDS) that can evolve to acute myeloid leukemia (AML). The MDS progression is usually associated with the acquisition of cytogenetic and/or additional somatic alterations. Mutations in SETBP1 and ASXL1 genes are frequently observed in pediatric GATA2 patients, although how they contribute to the disease progression remains poorly understood. Here we develop a human induced pluripotent stem cells (hiPSCs)-based model to study the impact of germline GATA2 mutation along with selected somatic mutations on GATA2 deficiency progression. We found that, while germline heterozygous GATA2 mutation alone is insufficient to induce an impairment of myeloid development, SETBP1 and ASXL1 mutations lead to a significant decrease of myeloid differentiation potential with a complete monocytopenia. The prominent loss of myeloid progenitor was associated with a down regulation of myeloid-specific genes and an up-regulation of leukemic stem cell markers. Through epigenomic profiling, we found that mutation in SETBP1 promotes chromatin remodeling in genes involved in myeloid neoplasms that preceded the blockage of myeloid differentiation, a state that persisted after the acquisition of the ASXL1 mutation. Finally, transcription factors motif analysis revealed an enrichment for MEIS1, PU.1, RUNX1 and HOXA9 motifs in more accessible chromatin regions, suggesting their cooperation in disease progression. Beyond establishing a valuable tool for studying the molecular mechanisms underlying GATA2 deficiency, our findings suggest that mutated SETBP1 primes the onset of hematopoietic impairment at transcriptomic and epigenomic level in GATA2 deficiency, a process exacerbated by the acquisition of the ASXL1 mutation.