Figure 3.
Immune biomarkers associated with response to ICB
(A) Association dot matrix showing the level and direction of association between each immune predictive biomarker (columns) and pCR in the population/model as labeled (rows). Only those biomarkers that were significant (p < 0.05; after Benjamini-Hochberg multiple testing correction) in at least one cohort are shown. ALL, Pembro Arm, multi-IF platform (n = 54 patients); ALL, Pembro Arm, mRNA platform (n = 69 patients); ALL, Pembro Arm, RPPA platform (n = 67 patients); ALL, Control, multi-IF platform (n = 44 patients); ALL, Control, mRNA platform (n = 179 patients); ALL, Control, RPPA platform (n = 169 patients); HR−HER2−, Pembro Arm, multi-IF platform (n = 24 patients); HR−HER2−, Pembro Arm, mRNA platform (n = 29 patients); HR−HER2−, Pembro Arm, RPPA platform (n = 27 patients); HR−HER2−, Control, multi-IF platform (n = 23 patients); HR−HER2−, Control, mRNA platform (n = 85 patients); HR−HER2−, Control, RPPA platform (n = 78 patients); HR+ HER2−, Pembro Arm, multi-IF platform (n = 30 patients); HR+ HER2, Pembro Arm, mRNA platform (n = 40 patients); HR+ HER2−, Pembro Arm, RPPA platform (n = 40 patients); HR+ HER2−, Control, multi-IF platform (n = 21 patients); HR+ HER2−, Control, mRNA platform (n = 94 patients); HR+ HER2−, Control, RPPA platform (n = 91 patients). Color of dot indicates direction of association (red, higher in pCR; blue, higher in non-pCR). Size of dot is proportional to significance (larger dots → smaller p values). Background square color indicates BH false discovery rate [FDR] p < 0.05 (white), nominal p < 0.05 (light gray), not significant (dark gray).
(B) Boxplots illustrating the associations of various biomarkers related to TILs, MHC class II, and other immune cell types with pCR in the Pembro arm. The data are depicted as individual dots for each sample, along with the median, first, and third quartile. Statistical analysis was performed using the likelihood-ratio test. ∗p < 0.05 (not corrected), ∗∗p < 0.05 (BH corrected).
(C) Boxplots illustrating the associations of various biomarkers related to PD-L1 and PD-1 expression with pCR in the Pembro arm. The data are depicted as individual dots for each sample, along with the median, first, and third quartile. Statistical analysis was performed using the likelihood-ratio test. ∗∗p < 0.05 (BH corrected).