SOD1 is a synthetic lethal target in PPM1D-mutant leukemia cells

Joint Public Review:

Strengths:

Gain-of-function mutations and amplifications of PPM1D are found across several human cancers and are associated with advanced tumor stage, worse prognosis, and increased lymph node metastasis. In this study, Zhang and colleagues investigate the synthetic-lethal dependencies of PPM1D (protein phosphatase, Mg2+/Mn2+ dependent 1D) in leukemia cells using CRISPR/Cas9 screening. They identified that SOD1 (superoxide dismutase-1) as the top hit, whose loss reduces cellular growth in PPM1D-mutant cells, but not wild-type (WT) cells. Consistently, the authors demonstrate that PPM1D-mutant cells are more sensitive to SOD1 inhibitor treatment. By performing different in vitro studies, they show that PPM1D-mutant leukemia cells have an elevated level of reactive oxygen species (ROS), decreased basal respiration, increased genomic instability, and impaired non-homologous end-joining repair. The data strongly support that PPMD1 mutant cells have high levels of total peroxides and elevated DNA breaks and that genetic depletion of SOD1 decreases cell growth in two AML cell lines. These data highlight the potential of SOD1 inhibition as a strategy to achieve therapeutic synergism for PPM1D-mutant leukemia; and demonstrate the redox landscape of PPM1D-mutant cells.

Weaknesses:

It is not explained how superoxide radical (which is not damaging by itself) induces damage, the on-target effects of the SOD1 inhibitors at the concentrations are not clear, the increase in total hydroperoxides is not supported by loss of SOD1, the changes in mitochondrial function are small, and there is no assessment of how the mitochondrial SOD2 expression or function, which dismutates mitochondrial superoxide, is altered. Overall these studies do not distinguish between signal vs. damaging aspects of ROS in their models and do not rule out an alternate hypothesis that loss of SOD1 increases superoxide production by cytosolic NADPH activity which would significantly alter ROS-driven regulation of kinase/phosphatase signal modulation, affecting cell growth and proliferation as well as DNA repair. Additionally, with the exception of growth defects demonstrated with sgSOD1, the majority of data are acquired using two chemical inhibitors, LCS1 and ATN-224, without supporting evidence that these inhibitors are acting in an on-target manner.

Overall, the authors address an important problem by seeking targetable vulnerabilities in PPM1D mutant AML cells. It is clear that SOD1 deletion induces strong growth defects in the AML cell lines tested, that most of the approaches are appropriate for the outcomes being evaluated, and that the data are technically solid and well-presented. The major weakness lies in which redox pathways and ROS species are evaluated, how the resulting data are interpreted, and gaps in the follow-up experiments. Due to these omissions, as currently presented, the broader impact of these findings is unclear.

Author Response:

We thank the editors and reviewers for their thoughtful and constructive assessment of our manuscript. In the upcoming revision process, we plan to address key concerns highlighted by the reviewers. While the bulk of our data involved the use of chemical SOD1 inhibitors, we intend to assess their on-target efficacy by measuring SOD activity after treatment. Additionally, we plan to perform key experiments to measure oxidative stress and DNA damage in SOD1-deletion cell lines to compare against the effects of chemical SOD1 inhibition. We acknowledge the lack of consideration for SOD2 and plan to explore changes in mitochondrial SOD2 expression and function in PPM1D-mutant cells at baseline and after SOD1-deletion. We will refine the text to clarify the data interpretation and elaborate on the limitations of our study in the discussion. Altogether, we thank the reviewers for their suggestions to improve our study and we hope that these additional experiments will provide additional evidence that SOD1 is a dependency in PPM1D-mutant leukemia cells.