Small Molecule Disrupts Abnormal Gene Fusion Associated with Leukemia

Disulfiram inhibits the binding of the NUP98-PHF23 fusion gene product to DNA of blood-forming cells, preventing the overexpression of certain kinds of genes associated with several types of leukemia, such as <em>Hoxa9</em>

Disulfiram inhibits the binding of the NUP98-PHF23 fusion gene product to DNA of blood-forming cells, preventing the overexpression of certain kinds of genes associated with several types of leukemia, such as Hoxa9.

Rare chromosomal abnormalities, called chromosomal translocations, in which part of a chromosome breaks off and becomes attached to another chromosome, can result in the generation of chimeric proteins. These aberrant proteins have unpredictable, and sometimes harmful, functions, including uncontrolled cell growth that can lead to cancer. One type of translocation, in which a portion of the gene encoding nucleoporin 98 (NUP98)—one of about 50 proteins comprising the nuclear pore complex through which proteins are shuttled into and out of the nucleus—fuses with another gene, has been shown to result in improper histone modifications. These abnormalities alter the gene expression patterns of certain types of hematopoietic, or blood-forming, stem cells, resulting primarily in overexpression of the Hoxa7, Hoxa9,and Hoxa10 genes. NUP98 chromosomal translocations have been associated with many types of leukemia, including acute myeloid leukemia (AML), acute lymphoid leukemia (ALL), chronic myeloid leukemia in blast crisis (CML-bc), and myelodysplastic syndrome (MDS).

When NUP98 fuses with a gene that encodes the chromatin binding protein PHF23, the result is production of an aberrant chromatin modifier. This NUP98-PHF23 (NP23) fusion leads to the overexpression of Hoxa9 and the overproliferation of myeloid progenitor cells that is linked to AML. Peter Aplan, M.D., Head of the Leukemia Biology Section in CCR’s Genetics Branch, and his colleagues generated transgenic mice that expressed the NP23 fusion gene in all hematopoietic tissues, and used global gene expression assays and chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-seq) to identify aberrant gene expression profiles and chromatin modifications associated with the NP23 fusion.

Gene expression profiles revealed overexpression of Hoxa/b, Meis1, and Bahcc1 genes in NP23 tissues. In addition, BAHCC1 overexpression occurred in a slightly different pattern than HOXA and MEIS1 in AML patients, pointing to the gene as a new marker for AML. Further analysis suggests that BAHCC1 overexpression is associated with HOXA expression patterns, but is not directly driven by the NP23 fusion.

Using ChIP-seq, Aplan’s team discovered that NP23 bound a chromatin mark of active gene transcription (H3K4me3) via the PHD-domain of the NP23 fusion protein, at specific sites, with highest levels at the loci of stem cell self-renewal genes including Hoxa, Hoxb, and Meis1. The researchers then evaluated five compounds that have recently been shown to inhibit H3K4me3 binding to the PHD domain in vitro. Of those compounds, disulfiram, an FDA-approved drug, was found to rapidly and selectively kill NP23 myeloblasts (immature white blood cells), but not control myeloblast cell lines. The researchers also found that disulfiram-mediated cell death was preceded by decreased expression of Hoxa, Hoxb, and Meis1, consistent with their proposed role in oncogenesis. In separate experiments, AML driven by the related fusion gene NUP98-JARID1A was found to also be sensitive to disulfiram. Levels of NP23 and NUP98-JARID1A fusion proteins bound to H3K4me were significantly reduced in disulfiram treated cells, suggesting that this compound may be useful for disrupting a variety of oncogenic PHD-domain proteins that play a role in cancer.

Taken together, the team’s findings suggest that inhibiting H3K4me3/PHD interactions of NP23 and NUP98-JARID1A fusion proteins with disulfiram reduces the expression of the oncogenic Hoxa, Hoxb, and Meis1 genes, providing a potential treatment for leukemic subtypes that are associated with the NUP98-PHF23 or NUP98-JARID1A fusions.

Summary Posted: Sat, 03/01/2014


Gough SM, Lee F, Yang F, Walker RL, Zhu YJ, Pineda M, Onozawa M, Chung YJ, Bilke S, Wagner EK, Denu JM, Ning Y, Xu B, Wang GG, Meltzer PS, Aplan PD. NUP98-PHF23 is a chromatin modifying oncoprotein that causes a wide array of leukemias sensitive to inhibition of PHD domain histone reader function. Cancer Discovery, February 17, 2014 PubMed Link