CHD1 - a Novel Epigenetic Regulator in Myeloid Malignancies with a Role in DNA Repair

Myelodysplastic syndromes (MDS) and acute myeloid leukemias (AML) are clonal hematopoietic disorders resulting from genetic alterations in hematopoietic stem cells. These myeloid disorders are clinically heterogeneous and biologically complex. Despite major advances in understanding the genetic and molecular landscape of MDS/AML, along with the introduction of newer and targeted therapies, the cure rates in AML are still only about 60% in children, and much lower in adults. Exploiting the genetic tractability of the zebrafish (Danio rerio) vertebrate model, we are investigating the role of a novel epigenetic regulator, Chromodomain helicase DNA binding protein-1 (CHD1) in hematopoiesis and its misregulation leading to MDS and AML. CHD1 is located at chromosome 5q21, which lies within the most frequent breakpoints seen with the deletion of the long arm of chromosome 5 [del (5q)] in patients with MDS and AML. In addition to del (5q), we found that CHD1 levels are significantly lower in bone marrow cells of patients with other forms of MDS, relative to normal controls. Using CRISPR/Cas9-mediated targeted mutagenesis in zebrafish, we created chd1 homozygous mutant fish. We confirmed a marked decrease in chd1 gene expression in these mutant fish. Chd1 homozygous mutants are viable and fertile as adults, with no significant developmental or hematopoietic phenotypes observed during embryogenesis. As CHD1 can act as a tumor suppressor and is linked to the DNA damage response, we hypothesized that chd1 mutant zebrafish would be more sensitive to DNA damaging agents. Indeed, we found that chd1 mutants have increased sensitivity to ionizing radiation as evidenced by elevated brain cell death measured by whole mount imaging of live embryos and immunofluorescence for activated Caspase 3, a marker of apoptosis. We also generated chd1^het; tp53^het zebrafish to test whether chd1 haploinsufficiency could accelerate tumor rates in tp53 mutant fish. Single heterozygotes chd1^het or tp53^het usually do not form tumors at one year of age, but chd1^het; tp53^het double heterozygous zebrafish showed substantial tumor growth by one year of age. Taken together, our data suggest that CHD1 may play a key role in protecting genomic integrity, explaining why diminished CHD1 levels could contribute to the pathogenesis of MDS and AML. This genetic interaction may be especially crucial in patients with combined del (5q) and TP53 alterations, and could contribute to the increased severity seen in this group. Our findings suggest these and other CHD1-deficient patients may be resistant to standard therapies due to attenuated DNA damage responses, allowing their AML to survive DNA damage caused by conventional anti-cancer treatments.