Niche-Based Screening Reveals Leukemia Stem Cell Specific Therapeutics
Authors: Hartwell Kimberly A. , Miller Peter G. , Stewart Alison L. , Kahn Alissa R. , Logan David J. , Negri Joseph , Duvet Mildred , Chattopadhyay Shrikanta , Shterental Sebastian , Chu Lisa P , Shieh Jae Hung , Jaeraas Marcus , Dancik Vladimir , Narayan Rajiv , Huang Christina , Haydu J Erika , Mukherjee Siddhartha , Shamji Alykhan F , Tolliday Nicola J , Carpenter Anne E. , Schreiber Stuart L. , Stern Andrew M. , Moore Malcolm AS , Scadden David T. , Ebert Benjamin L. , Golub Todd R. 
Published: October 2019

Abstract
Abstract 760
Recent insights into the molecular and cellular processes that drive leukemia have called attention to the limitations intrinsic to traditional drug discovery approaches. To date, the majority of cell-based functional screens have relied on probing cell lines in vitro in isolation to identify compounds that decrease cellular viability. The development of novel therapeutics with greater efficacy and decreased toxicity will require the identification of small molecules that selectively target leukemia stem cells (LSCs) within the context of their microenvironment, while sparing normal cells.
We hypothesized that it would be possible to systematically identify LSC susceptibilities by modeling key elements of bone marrow niche interactions in high throughput format. We tested this hypothesis by creating and optimizing an assay in which primary murine stem cell-enriched leukemia cells are plated on bone marrow stromal cells in 384-well format, and examined by a high content image-based readout of cobblestoning, an in vitro morphological surrogate of cell health and self-renewal. AML cells cultured in this way maintained their ability to reinitiate disease in mice with as few as 100 cells.
14,720 small molecule probes across diverse chemical space were screened at 5uM in our assay. Retest screening was performed in the presence of two different bone marrow stromal types in parallel, OP9s and primary mesenchymal stem cells (MSCs). Greater than 60% of primary screen hits positively retested (dose response with IC50 at or below 5 μM) on both types of stroma. Compounds that inhibited leukemic cobblestoning merely by killing the stroma were identified by CellTiter-Glo viability analysis and excluded. Compounds that killed normal primary hematopoietic stem and progenitor cell inputs, as assessed by a related co-culture screen, were also excluded. Selectivity for leukemia over normal hematopoietic cells was additionally examined in vitro by comingling these cells on stroma within the same wells. Primary human CD34+ AML leukemia and normal CD34+ cord blood cells were also tested, by way of the 5 week cobblestone area forming cell (CAFC) assay. Additionally, preliminary studies of human AML cells pulse-treated with small molecules ex vivo, followed by in vivo transplantation, provided further evidence of potent leukemia kill across genotypes.
A biologically complex functional approach to drug discovery, such as the novel method described here, has previously been thought impossible, due to presumed incompatibility with high throughput scale. We show that it is possible, and that it bears fruit in a first pilot screen. By these means, we discover small molecule perturbants that act selectively in the context of the microenvironment to kill LSCs while sparing stroma and normal hematopoietic cells. Some hits act cell autonomously, and some do not, as evidenced by observed leukemia kill when only the stromal support cells are treated prior to the plating of leukemia. Some hits are known, such as parthenolide and celastrol, and some are previously underappreciated, such as HMG-CoA reductase inhibition. Others are entirely new, and would not have been revealed by conventional approaches to therapeutic discovery. We therefore present a powerful new approach, and identify drug candidates with the potential to selectively target leukemia stem cells in clinical patients.

Disclosures:
No relevant conflicts of interest to declare.