Gene Regulatory Networks in Acute Myeloid Leukemia: Elf1 a Regulator of Myeloid Innate Immunity

Acute Myeloid Leukemia (AML) is a life-threatening disease caused by diverse genetic alterations that result in the accumulation of undifferentiated cells of myeloid lineage in the bone marrow. A detailed understanding of the molecular mechanisms responsible for these genetic aberrations is necessary to interpret the regulatory networks within AML and develop suitable drug targets. Though Elf1 (E74-like factor-1) is universally overexpressed in the majority of AMLs, the involvement of this transcription factor in leukemias is not well studied. This doctoral thesis aimed to elucidate the role of Elf1 in the complex gene regulatory network of AML. Elf1 is a common target gene of two leukemogenic oncoproteins, the homeobox gene HoxA9 and the chromosomal translocation product MLLENL. Chromatin immune precipitation of MLLENL/HoxA9 and targeted time-course transcriptomic analysis of Elf1 after degradation of these oncoproteins revealed that HoxA9 and MLL fusions bind to regulatory regions of Elf1 and control its gene expression. Similarly, Elf1 ChIP results disclosed that Elf1 mainly binds in the enhancer/promoter regions of the chromatin and colocalizes with HoxA9 and its collaboration partner Meis1. Here, Elf1 utilizes HoxA9-defined open chromatin and participates in the myeloid enhancer framework. Significant Elf1 binding was also observed at the known hematopoietic enhancer of Myc and in the enhancer region of Nfkb pathway members Nfkb2 and RelB. Gene expression profile of Elf1 was established by sequencing nascent RNA before and after the degradation of Elf1 in an endogenous Elf1-depleted background. Next-generation sequencing data comparing genes activated versus repressed by Elf1 revealed that this regulatory protein controls a transcription program dominated by genes of innate immunity, with Nfkb2, RelB and its inhibitors Nfkbia and Nfkbie as prime examples. LPS stimulation experiments and luciferase reporter assays supported the finding that ELF1 is necessary for the activation of the Nfkb noncanonical signaling pathway in response to an immunogenic stimulus. ELF1 knockdown cells increased the sensitivity to the chemotherapeutic agent doxorubicin and also reduced MOLM13 human AML cell proliferation. Interestingly, a point mutation introduced in Elf1’s most active phosphorylation site (S187A) altered Elf1's regulatory activity on Nfkb2/RelB promoters. This study highlights the importance of Elf1 in AML gene regulatory networks and myeloid innate immunity. Clinical importance of Nfkb2’s role in inducing chemoresistance, along with RelB’s association with negative patient survival and involvement of Elf1 in regulating these target genes, requires further exploration.