Simultaneous Monitoring of Drug Responses on Distinct Hematopoietic Cell Populations Allow Assessment of Direct and Indirect Cytotoxic Effects of Targeted Therapies

Introduction

Off-target cytotoxicity resulting in severe side effects and compromising patient survival often hampers the development of new cancer therapeutics. Understanding the complete drug response landscape of different cell populations is crucial to identify drugs that selectively eradicate the malignant cell population, but spare healthy cells. Here, we developed a high content, no wash, multi-parametric flow cytometry based assay that enables testing of blood cancer patient samples and simultaneously monitors the effects of several drugs on 11 hematopoietic cell types. The assay can be used to i) dissect malignant from healthy cell responses and predict off-target effects; ii) assess drug effects on immune cell subsets; iii) identify drugs that can potentially be repositioned to new blood cancer indications.

Methods

Mononuclear cells were prepared from bone marrow aspirates of 7 multiple myeloma (MM) and 3 acute myeloid leukemia (AML) patients plus the peripheral blood from a healthy donor, which were collected following informed consent and in compliance with the Declaration of Helsinki. Optimal cell density, antibody dilutions, incubation time, and wash versus no wash assay conditions for the selected antibody panels were determined. Cells were incubated at a density of 2 million cells/ml in either 96- or 384-well plates for 3 days. The antibodies were tested in two panels to study the effects of 6 drugs in 5 dilutions (1-10000 nM) (clofarabine, bortezomib, dexamethasone, navitoclax, venetoclax and omipalisib) on 11 cell populations, namely hematopoietic stem cells (HSCs) (CD34+CD38-), common progenitor cells (CPCs) (CD34+CD38+), monocytes (CD14+), B cells (CD45+CD19+), cytotoxic T cells (CD45+CD3+CD8+), T helper cells (CD45+CD3+CD4+), NK-T cells (CD45+CD3+CD56+), NK cells (CD45+CD56+CD3-), clonal plasma cells (CD138+CD38+), other plasma cells (CD138+CD38-) and granulocytes (CD45+, SSC++). Annexin-V and 7AAD were used to distinguish live cell populations from apoptotic and dead cells. After 1 h incubation with antibodies, the plates were read with the iQue Screener PLUS instrument (Intellicyt). Counts for each population were used to generate four parameter nonlinear regression fitted dose response curves with GraphPad Prism 7. Three samples were tested in duplicate to assess reproducibility.

Results

To decrease the complexity of the assay, we tested all antibodies under wash and no wash conditions, and found that results from both conditions were comparable. To minimize the amount of sample needed as well as maximize the number of drugs tested and cell populations that can be detected, we set up the assay in both 96- and 384-well plates. The assay was highly reproducible when samples were tested in replicate and was scalable to a 384-well format without compromising sensitivity to detect rare populations such as plasma cells. Due to the differentiation of immature cells to specialized cell types, the drug responses of specific populations tended to drift. HSCs (CD34+CD38-) were shown to be refractory to the tested drugs compared to CPCs characterized as (CD34+CD38+) and other cell types. Interestingly, the proteasome inhibitor bortezomib was cytotoxic to all cell populations except for CD138+CD38- plasma cells. Clofarabine, a nucleoside analog used to treat ALL, effectively targeted CPC, NK and B cells, while HSCs and plasma cells were resistant. The glucocorticoid and immunosuppressive drug dexamethasone specifically targeted B and NK cells compared to T cell populations (CD8+, CD4+), while NK-T cells were modestly sensitive. The cell population response patterns were similar in samples derived from MM, AML and healthy individuals, highlighting that the drug responses are highly cell type specific.

Summary

Using a high content, multi-parametric assay, we could rapidly assess the effect of several drugs on specific cell populations in individual patient samples. Our results demonstrate that many drugs preferentially affect different hematological cell lineages. Although heterogeneity was observed between individual patients, the pattern of cytotoxic response exhibited by specific cell types was consistent among samples derived from MM, AML and healthy donors. The assay will be useful to identify drugs with maximal on-target and minimal off-target specificity, and can potentially be used to guide treatment decision and predict patient response