Extended Data Fig. 4: Pre-therapy CD8 Teff cell IRC correlates to patient survival following anti-PD1 therapy across the cohorts.
a. Median IFNAR1 expression for each patient in the indicated cluster of CD4 T cells from the Discovery cohort direct ex vivo dataset (from Fig. 1b), comparing patients with high (n = 11) versus low (n = 20) CD4 Teff IRC. Boxes show median, upper and lower quartile and whiskers show 1.5x the interquartile range on either side. b. Circulating IFNγ levels were measured in the serum of patients at baseline by Luminex multi-plex ELISA (n = 26; excluding five patients with out of range readings) and stratified into high or low IRC groups based on the individual patients CD4 Teff cell IRC. Boxes show median, upper and lower quartile and whiskers show 1.5x the interquartile range on either side. c. Proteins used to classify T cell subsets. d. Expression of the indicated protein in CD4 T cell clusters (top panels) and CD8 T cell clusters (bottom panels) from the Discovery cohort after overnight culture. e. Kaplan–Meier curves showing overall survival (OS) in the Discovery cohort based on pre-therapy high versus low IRC of the CD8 Teff cell population. t0 is the number of patients in each group at time zero. f. Proteins used to classify T cell subsets in the melanoma and lung validation cohorts. g. Kaplan–Meier curve comparing OS of patients with low or high IRC in the CD8 Teff cells in the melanoma validation cohort (left) and NSCLC validation cohort (right). (e, g) Two-sided log-rank P value is shown.
