Abstract
Targeted therapies exploiting vulnerabilities of cancer cells hold promise for improving patient outcome and reducing side effects of chemotherapy. Despite a high response rate to induction chemotherapy in acute lymphoblastic leukemia (ALL) there is an urgent need to identify effective combination therapy to overcome treatment resistance that associates with disease relapse.
ALL cells are acutely highly sensitive to the WEE1 inhibitor AZD1775 that compromises the G2/M-phase cell cycle checkpoint. Here, we show that AZD1775 selectively inhibits recovery of proliferation in KMT2A/MLL-rearranged (MLL-r) ALL, a group of leukemias that respond poorly to current chemotherapy and have dismal prognosis compared to other leukemia subgroups. This vulnerability could be distinguished by elevated WEE1 expression in MLL-r ALL and through biochemical analysis of the resulting mitotic catastrophe upon WEE1 inhibition as assessed by PARP cleavage and flow cytometric analysis of DNA metabolism.
Extensive genomics profiling of the drug response by joint single-cell transcriptome and chromatin accessibility profiling revealed that AZD1775 led to a strong p53-driven gene regulatory response resulting in induction of apoptosis and senescence and disrupts a crucial hematopoietic TF-network involving RUNX1, MYC and GATA2. We further demonstrate that RUNX1 protein was degradaded in a CDK-dependent manner.
Leukemia relapse may arise from rare cells that escape treatment through genetic mutations, transcriptional reprogramming or signaling rewiring. We here demonstrate that upon the pre-mature mitosis entry resulting from AZD1775 treatment, a rapid transcriptional reprogramming is triggered involving activation of NfKB and transcription factors regulating lipid metabolism, BCL6 and pre-BCR signaling that resulted in a small surviving cell population. Single-cell characterization of the AZD1775 response in a MLL-r patient-derived xenograft (PDX) model supported the in vivo relevance of this drug resistance mechanism. Informed by the genomic profiles, sequential administration of AZD1775 with inhibitors of pre-BCR signaling or fatty acid synthesis was designed to target the resistant cell state and this approach effectively prevented cell survival and recovery of ALL cells.
Collectively, our findings provide new insights into the tight connectivity of gene regulatory programs associated with cell survival and cell fate regulation in response to drugs targeting cell cycle regulation and provide a rationale for combination therapies with low toxicity drugs such as dasatinib or fatostatin to counteract drug resistance that occurs through cell state switching.
Disclosures
No relevant conflicts of interest to declare.
Author notes
Asterisk with author names denotes non-ASH members.
