Comparing the value of mono- vs coculture for high-throughput compound screening in hematological malignancies

Abstract

Large-scale compound screens are a powerful model system for understanding variability of treatment response and for discovering druggable tumor vulnerabilities of hematological malignancies. However, as mostly performed in a monoculture of tumor cells, these assays disregard modulatory effects of the in vivo microenvironment. It is an open question whether and to what extent coculture with bone marrow stromal cells could improve the biological relevance of drug testing assays over monoculture. Here, we established a high throughput platform to measured ex vivo sensitivity of 108 primary blood cancer samples to 50 drugs in monoculture and in coculture with bone marrow stromal cells. Stromal coculture conferred resistance to 52 % of compounds in chronic lymphocytic leukemia (CLL) and to 36 % of compounds in acute myeloid leukemia (AML), including chemotherapeutics, BCR inhibitors, proteasome inhibitors and BET inhibitors. While most of the remaining drugs were similarly effective in mono- and coculture, oOnly the JAK inhibitors ruxolitinib and tofacitinib exhibited increased efficacy in AML and CLL stromal coculture. We further confirmed the importance of JAK-STAT signaling for stroma-mediated resistance by showing that stromal cells induce phosphorylation of STAT3 in CLL cells. We genetically characterized the 108 cancer samples and found that drug-gene associations agreed strongly correlated well between mono- and coculture. OverallHowever, effect sizes were lower in coculture, thus with more drug-gene associations were detected in monoculture than in coculture. Our results suggest justifies a two-step strategy for drug perturbation testing, with large-scale screening performed in monoculture, followed by focused evaluation of potential stroma-mediated resistances in coculture. -

Morphological profiling for drug discovery in the era of deep learning

“…Applying relevant cell types and perturbations in morphological profiling assay is essential, but not sufficient to guarantee translatability [ 1 ]. Recent efforts have been made to apply increasingly multiplex biological model systems for image-based profiling, such as cocultured 2D cell lines [ 151 ] and 3D organoids [ 152 , 153 ]. However, on the computational side, most approaches have been built upon Cell Painting assay images from mono-cultured 2D cells.…”

Pre-Clinical Assessment of SAR442257, a CD38/CD3xCD28 Trispecific T Cell Engager in Treatment of Relapsed/Refractory Multiple Myeloma

“…We evaluated the linear correlations between CD28 and CD38 target expression, as well as the linear correlations of drug response and TC activation and the correlations between target expression and MM cell death, using the Pearson correlation coefficient. The Pearson correlation measures the strength and direction of the linear relationship between two variables, allowing for comparison of the degree of linear association between drug response profiles across different cell lines and patients [40]. Statistical details have been provided in the figures and figure legends.…”

Conditional lethality profiling reveals anticancer mechanisms of action and drug-nutrient interactions

“…Nonetheless, while recent work has shown that in vitro drug treatment phenotypes can depend on relative oxygen tension 22 , the presence of stromal cells 23,24 , and culture in 3D models [25][26][27][28] , there has been considerably less attention on the influence of medium composition 29 -arguably the most flexible component of the in vitro environment.…”