Abstract
Breakpoint Cluster Region-Abelson kinase (BCR–Abl) is a driver oncogene that causes chronic myeloid leukemia and a subset of acute lymphoid leukemias. Although tyrosine kinase inhibitors provide an effective treatment for these diseases, they generally do not kill leukemic stem cells (LSCs), the cancer-initiating cells that compete with normal hematopoietic stem cells for the bone marrow niche. New strategies to target cancers driven by BCR–Abl are therefore urgently needed. We performed a small molecule screen based on competition between isogenic untransformed cells and BCR–Abl-transformed cells and identified several compounds that selectively impair the fitness of BCR–Abl-transformed cells. Interestingly, systems-level analysis of one of these novel compounds, DJ34, revealed that it induced depletion of c-Myc and activation of p53. DJ34-mediated c-Myc depletion occurred in a wide range of tumor cell types, including lymphoma, lung, glioblastoma, breast cancer, and several forms of leukemia, with primary LSCs being particularly sensitive to DJ34. Further analyses revealed that DJ34 interferes with c-Myc synthesis at the level of transcription, and we provide data showing that DJ34 is a DNA intercalator and topoisomerase II inhibitor. Physiologically, DJ34 induced apoptosis, cell cycle arrest, and cell differentiation. Taken together, we have identified a novel compound that dually targets c-Myc and p53 in a wide variety of cancers, and with particularly strong activity against LSCs.
Highlights
Breakpoint Cluster Region-Abelson kinase (BCR–Abl) is the driver mutation for chronic myeloid leukemia (CML) and is found in 25% to 30% of Philadelphia chromosome– positive (Ph+) adult acute lymphoid leukemia (ALL) [1, 2]
To identify novel compounds that target BCR–Abl-driven leukemias, we developed an isogenic cell competition–based drug screen by stably transfecting Ba/F3 cells with BCR–Abl
These cells were mixed and treated with imatinib for 72 h, after which the BCR– Abl:WT cell ratio was measured by flow cytometry (Fig. 1B)
Summary
To identify novel compounds that target BCR–Abl-driven leukemias, we developed an isogenic cell competition–based drug screen by stably transfecting Ba/F3 cells with BCR–Abl. We screened 17,962 compounds for selective inhibition of BCR–Abl-expressing cells (Fig. 1E). We selected 203 compounds that fell outside the 3σ interval (Fig. 1G) These compounds were retested three times, resulting in 87 drugs that significantly (p < 0.05) altered the BCR–Abl:WT cell ratio (Fig. 1H). We identified eight compounds that reduced the competitiveness of BCR–Abl cells, including sobuzoxane (topoisomerase II inhibitor) and the phosphodiesterase inhibitor isobutylmethylxanthine (Fig. 2) Their effect was validated by unrelated inhibitors (Fig. S2, A–E). Six uncharacterized compounds selectively inhibited BCR– Abl-expressing cells (DJ1, DJ2, DJ3, DJ12, DJ34, and DJ35; Fig. 2), but they did not directly target BCR–Abl (Fig. S3). Treatment with DJ34 promoted the expression of genes that are inhibited by c-Myc,
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