Fig. 2.
Reliability of the Beyondcell score and its application in cancer cell lines under drug exposure. a Median BCS obtained with SSC signatures for cells at t0 correlate negatively (R = − 0.19, p = 8e−03) with MCF7-AA viability measures reported by Ben-David et al. [16]. b Using BCS obtained with PSC signatures, Beyondcell is capable of clustering MCF7-AA cells treated with bortezomib [16] into therapeutic clusters that overlap with treatment times. Left: UMAP plot of the integrated Seurat object coloured by treatment time; Centre: UMAP plot of the Beyondcell object also coloured by treatment time; Right: UMAP plot of the Beyondcell object coloured by bortezomib BCS. Untreated cells (t0) are sensitive to bortezomib whereas cells undergoing treatment (t12 and t48) are insensitive. After treatment during 72 h followed by drug wash and 24 h of recovery, cells at 96 h (t96) restore their sensitivity to this drug. c Beyondcell UMAP plot for the Ho et al. [17] dataset and the SSC drug signatures. Top left: cells coloured according to the treatment condition; Top right: cells coloured by Beyondcell’s therapeutic clusters; Bottom: Beyondcell UMAP plot showing the summed expression of several BRAF inhibitor-resistant biomarkers (JUN, WNT5A, PDGFRB, EGFR, NRG1, FGFR1 and AXL). d Histogram representing trametinib Beyondcell scores in each therapeutic cluster