A multiparametric niche-like drug screening platform in acute myeloid leukemia

Abstract

Functional precision medicine in AML often relies on short-term in vitro drug sensitivity screening (DSS) of primary patient cells in standard culture conditions. We designed a niche-like DSS assay combining physiologic hypoxia (O2 3%) and mesenchymal stromal cell (MSC) co-culture with multiparameter flow cytometry to enumerate lymphocytes and differentiating (CD11/CD14/CD15+) or leukemic stem cell (LSC)-enriched (GPR56+) cells within the leukemic bulk. After functional validation of GPR56 expression as a surrogate for LSC enrichment, the assay identified three patterns of response, including cytotoxicity on blasts sparing LSCs, induction of differentiation, and selective impairment of LSCs. We refined our niche-like culture by including plasma-like amino-acid and cytokine concentrations identified by targeted metabolomics and proteomics of primary AML bone marrow plasma samples. Systematic interrogation revealed distinct contributions of each niche-like component to leukemic outgrowth and drug response. Short-term niche-like culture preserved clonal architecture and transcriptional states of primary leukemic cells. In a cohort of 45 AML samples enriched for NPM1c AML, the niche-like multiparametric assay could predict morphologically (p = 0.02) and molecular (NPM1c MRD, p = 0.04) response to anthracycline-cytarabine induction chemotherapy. In this cohort, a 23-drug screen nominated ruxolitinib as a sensitizer to anthracycline-cytarabine. This finding was validated in an NPM1c PDX model.

Designing patient-oriented combination therapies for acute myeloid leukemia based on efficacy/toxicity integration and bipartite network modeling

“…Numerous studies show the signi cance of the JAK/STAT signaling system in determining how hematopoietic cells react to various cytokines and growth factors 21,22 . Recently there has been increased interest in different drug combinations with ruxotinib [23][24][25][26] and as our results show the combinations of this drug, by having the lowest toxicity, seems to be promising for AML treatment.…”

Drug combinations screening using a Bayesian ranking approach based on dose–response models

“…Figure 2c and d and Supporting Information Figures S1 and S2 represent the dose-response curves of the real data motivating example. We hypothesize the somewhat spiky behaviors observed may be related to various sources of variability in the experimental conditions (Dal Bello et al, 2022). In fact, the culture of primary AML cells is notoriously challenging, especially in the setting of relapse or refractory disease.…”

“…This work was motivated by an ongoing pilot experiment with a diagonal design for ex vivo drug screening on leukemia cells sampled from bone marrow or peripheral blood of AML patients (NCT05326919), using an established drug screening niche‐like platform (Dal Bello et al., 2022). The study was approved by INSERM (Institut National de la Santé Et de la Recheche Médicale) institutional review board (CEEI‐15‐220).…”

Novel precision medicine approaches and treatment strategies in hematological malignancies

“…Next‐generation drug testing assays provide single‐cell resolution using flow cytometry or imaging and support the ability to measure cell‐type specific responses and use nonmalignant cells from the same specimens as general toxicity controls [191]. These rely on the identification of blasts through the expression of cell surface markers or cellular morphology.…”