Extended Data Fig. 9: Immune infiltrates by flow cytometry analysis in resected uninvolved lungs and tumors treated with neoadjuvant Nivo+CT and Ipi+Nivo+CT.
a-h, Flow cytometry in paired resected uninvolved lung (n = 9) and tumor tissues (n = 9) in Nivo+CT. Percentage of CD4+ (Non Treg) ICOS+ TILs (a), CD4+ Treg TILs (b), CD8+ ICOS+ TILs (c), CD8+ ICOS+ Ki67+ TILs (d), CD4+ CD45RO+ CD27+ TILs (e), CD8+ CD45RO+ CD27+ TILs (f), CD8+ CTLA-4+ TILs (g), CD8+ CD103+ LAG3+ TILs (h). i-l, Flow cytometry in paired resected uninvolved lung (n = 6) and tumor tissues (n = 6) in Ipi+Nivo+CT. Percentage of CD4+ (Non Treg) ICOS+ TILs (i), CD8+ CD103+ (tissue-resident memory T cells, TRM) TILs (j), CD4+ CD45RO+ CD27+ TILs (k), CD8+ CD45RO+ CD27+ TILs (l). m-o, Flow cytometry in resected tumor tissues after Nivo+CT (n = 9) and Ipi+Nivo+CT (n = 6 in m and n, n = 5 in o) treatments. Percentages (top panels) and representative gates (bottom panels) of CD8+ ICOS+ Ki67- TILs (m), CD4+ (Non Treg) LAG3+ TILs (n), CD8+ Perforin+ TILs (o). The green filled and empty circles depict data from MPR and no MPR, respectively, in Nivo+CT patients, and the red filled and empty circles depict data from MPR and no MPR, respectively, in Ipi+Nivo+CT patients. Data are presented as the median with minima, lower and upper quartiles, and maxima using violin plots. The dashed line shows the median value, and dotted lines show the lower quartile and upper quartile values of the range; the top and bottom of the violin plots indicate the maxima and minima. Two-sided P value is from Wilcoxon signed-rank test (a-l) and Wilcoxon rank-sum test (m-o). Experiments and gating related to presented results were conducted once. Subgating was performed only when more than 100 events were present in the parental gate. Nivo, nivolumab; Ipi, ipilimumab; CT, chemotherapy; TILs, tumor-infiltrating lymphocytes; MPR, major pathologic response. Source data is provided as Source Data file.
