Extended Data Fig. 5: Population RNAseq analysis.
a-b, Graphical representations of the standard and multi-arm treatment models and resulting PCA analysis. In the standard model (a) matching d0 and d28 cells harvested from untreated (n = 37) and treated (n = 17) mice were analyzed. Untreated samples, shown in light blue, represent d0 cells from untreated mice and treated mice as well as d28 samples from untreated mice. In the multi-arm model (b), two consecutive rounds of transplantation and treatment (7 days) allowed the analysis of ‘acutely treated’ (n = 8 samples; green), ‘treatment withdrawn’ (n = 6 samples; dark yellow), ‘chronically treated’ (n = 5 samples; red), and ‘untreated control’ (n = 5 samples; dark blue) cells harvested from n = 3 mice each (see main text). ‘Relapse-like’ cells were also obtained through a separate arm of the experiment, whereby n = 3 mice were treated for 28 days and then let to relapse in situ in the absence of further treatment (6–8 weeks). c, Untreated and treated cells from primary recipients of Pt2 cells were transplanted into secondary recipients at three different limiting doses (100, 1*103, 1*104 cells). Engraftment (%) of BM, spleen and brain was assessed by flow cytometry and is shown in the dot plot (n = 4 mice for control; n = 5 mice for treated 100 and 1*103 cells; n = 4 mice for treated 1*104 cells). d, Estimated LIC frequencies for treated and untreated cell populations from each analyzed tissue (n = 4 mice for control; n = 5 mice for treated 100 and 1*103 cells; n = 4 mice for treated 1*104 cells) as calculated using the ELDA software69. In the top plot the number of initially injected cells (x-axis) is plotted against the log fraction of non-responders, corresponding to mice with no engraftment (y-axis).
