Background: Pediatric acute myeloid leukemia (AML) is a rare disease with roughly 500 cases diagnosed in the United States each year and has had minimal improvement in clinical outcomes over recent decades. Novel treatment development to improve outcomes may be enhanced with an accompanying test for predicting treatment response. We previously demonstrated that an ex vivo drug sensitivity assay (DSA) can predict clinical response in myelodysplastic syndrome. Here we investigated the use of the DSA in pediatric AML patients, including a subset participating in a clinical trial of atovaquone. Atovaquone is an FDA-approved anti-parasitic drug that was associated with lower relapse rates in adult AML patients. Adding atovaquone and other standard of care combination treatments into the DSA, we investigated whether the assay, performed on pre-induction samples, correlated with measures of clinical response. Methods: We assayed pre-induction blood or bone marrow samples from 22 de novo pediatric AML patients diagnosed at Texas Children’s between 5/2015 and 10/2020 who consented to research (82% enrolled in clinical trial identifier NCT03568994). We subsetted this analysis to patients who received ADE (Cytarabine, Daunorubicin, Etoposide) (n = 20) induction, with the majority additionally receiving atovaquone (n = 16). For the DSA, samples were incubated with up to 25 compounds, including the treatment drug combinations and each of the compounds individually. After incubation, changes in tumor blast populations were assessed by flow cytometry. For each drug condition, drug sensitivity was calculated based on the number of blasts remaining after treatment. After quality control, downstream analyses were limited to 13 samples. Clinical response data, including minimal residual disease (MRD) percentage by flow cytometry and one year relapse-free survival, were correlated with the drug sensitivity results. Results: For the de novo subset analysis, we observed correlations between ex vivo drug sensitivity with both MRD percentage (r = 0.63) and one year relapse-free survival (RFS1, AUC = 0.92). The 3 patients with lowest ex vivo sensitivity had the highest MRD percentages (mean 21%). 2 of the 3 patients who did not achieve one year relapse-free survival had the lowest ex vivo sensitivity. Drug combination sensitivity correlated more with MRD and RFS1 than the single agents alone (single agent mean MRD r = 0.39). Conclusions: In our cohort, ex vivo DSA for ADE and atovaquone in pediatric AML cases correlated with both MRD and one year relapse-free survival. This suggests that clinical response in pediatric AML may be assessed prior to treatment using a DSA. This study also suggests that the DSA can be used to test drug combinations, and thus may be used for investigating novel treatment combinations. Further development of the DSA may benefit treatment decisions and prioritization of drug development.
