Extended Data Fig. 5: Differential abundance analyses for immune subpopulations comparing rapid progressors versus non-progressors.
(a-d) Summary differential abundance volcano plots and individual cluster box plots, computed as either a fraction of (a) all immune cells, (b) B cells, (c) myeloid cells, or (d) CD3+ cells, comparing RP and NP patients. Each panel consists of a volcano plot in the top left, displaying the log-odds ratio (x-axis) derived from a site-adjusted linear model associating progression group with logit-transformed cell proportions, and the y-axis displays the -log10 of the two-sided p-value from the linear model. Points are colored according to cluster identity in Fig. 2. Box plots depict the per-patient proportion for each cluster within each compartment, with individual patients shown as open circles (Rapid Progressors (RP, npatient = 67)=Orange, Non-Progressors (NP, npatient = 83)= Blue). Two-sided p-values are displayed above the box plot if the populations are significantly different between RP and NP (p < 0.05) as assessed using a linear model. In the box plots, bounds of the box represent the 25th and 75th percentile, with the center displaying the median. Whiskers extend to 1.5*IQR beyond the bounds of the box. (e) Comparison of differential abundance profiles between triplet therapy patients and the overall cohort. The x and y axes display log-odds ratio change in proportion between RP (positive) and NP (negative) patients across triplet therapy patients (x-axis) or all patients (y-axis) as a fraction of immune cells.
