Chromatin Remodeling in ASXL1-mutant Chronic Myelomonocytic Leukemia

Histone modifications in promoter regions and de novo accessibility of genotype-specific distal enhancers strongly associate with leukemogenic gene expression.

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Chronic myelomonocytic leukemia (CMML) is an aggressive myeloid neoplasm for which currently no effective therapies exist. Particularly patients with truncating mutations in ASXL1 do not fare well and the development of novel therapeutic approaches remains an unmet clinical need.1 The chromatin modifier ASXL1 is involved in the maintenance of balanced gene expression of leukemogenic driver genes such as posterior HOXA cluster genes. Mechanistic studies suggest that ASXL1 has a complex interactome and that truncating ASXL1 mutations recruit several effectors to alter the epigenome through histone modifications, increases in chromatin accessibility, and remodeling of enhancers.2-4 ASXL1-mutant CMML represents a high-risk disease subtype characterized by an overexpression of leukemogenic driver genes that promote disease proliferation, therapeutic resistance, and transformation to acute myeloid leukemia. In this study, we interrogated the genome, transcriptome, and epigenome of patients with ASXL1-mutant CMML to learn more about the epigenetic determinants of leukemogenic gene expression in this patient population.

 

 

By comparing CMML patients with and without ASXL1 mutations, we identified several effects that ASXL1 mutations have on the epigenome and transcriptome of malignant monocytes in the bone marrow. We observed widespread chromatin remodeling and characteristic changes in gene expression that are consistent with the known proliferative disease phenotype (e.g. the overexpression of mitotic kinases). To understand how these changes in gene expression are supported by the epigenome, we interrogated histone modifications, DNA methylation, and DNA accessibility. We observed a strong effect of histone modifications in promoter regions and distal enhancers on the expression of important leukemogenic driver genes. In promoter regions of many overexpressed genes, a transition from poised and inactive chromatin states to active chromatin states was observed. This was mainly driven by increases in histone 3 lysine 27 acetylation (H3K27ac) and decreases in histone 3 lysine 27 trimethylation (H3K27me3). Importantly, these chromatin state transitions were quite heterogenous across the spectrum of overexpressed genes and did not necessarily reflect the global trends observed across the entire epigenome.

 
 
The de novo accessibility of distal enhancers in patients with ASXL1-mutant CMML was also strongly associated with the overexpression of their putative target genes. We identified several de novo accessible distal enhancers in proximity to overexpressed leukemogenic driver genes within the same topologically associating domains. These ASXL1-mutant specific distal enhancers were found to bind a restricted repertoire of transcription factors including ETS family members. Single-cell studies allowed us to validate these findings and to further investigate how ASXL1-specific changes in DNA accessibility alter the availability of transcription factor binding sites in distal enhancers. We observed markedly increased intratumoral heterogeneity in patients with ASXL1-mutant CMML due to an increase in accessible transcription factor binding sites. Despite the increased availability of transcription factor binding sites in ASXL1-mutant CMML, the spectrum of implicated transcription factors remained restricted and again included several of the previously identified ETS family members.

 

 

Overall, this study supports the notion that genotype-specific distal enhancers have a specific repertoire of transcription factors binding to them, strongly associate with the overexpression of important leukemogenic driver genes in their proximity, and may be attractive therapeutic targets for novel epigenetic small molecule drugs. These  ASXL1-mutant-specific distal enhancers and their interacting transcription factors may represent sufficiently lineage- and genotype-specific therapeutic targets to allow the development of safe and effective individualized therapies for patients with ASXL1-mutant CMML.

 

References 
1. Patnaik et al. ASXL1 and SETBP1 mutations and their prognostic contribution in chronic myelomonocytic leukemia: a two-center study of 466 patients. Leukemia 2014;28(11):2206-2212. 
2. Abdel-Wahab et al. ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell 2012;22(2):180-193.
3. Balasubramani et al. Cancer-associated ASXL1 mutations may act as gain-of-function mutations of the ASXL1-BAP1 complex. Nat Commun 2015;6:7307.
4. Yang et al. Gain of function of ASXL1 truncating protein in the pathogenesis of myeloid malignancies. Blood 2018;131(3):328-341.

Moritz Binder

Assistant Professor of Medicine, Mayo Clinic

I am a physician scientist specializing in hematologic malignancies.