Differential gene expression analysis identifies CD69 expression in CD8 T cells as a predictor of NSR. (A) Plot showing the preranked gene set enrichment analysis results for comparison of patients with SCROT vs those with NSR in lymphoid cells and CD14⁺ monocytes clusters. Dot size represents the normalized enrichment score (NES). Dot color represents the sign of the log fold change ∗ log10(false discovery rate [FDR] value) (ie, blue indicates enrichment in patients with SCROT and red indicates enrichment in patients with NSR). Only gene sets with NES >1.5 and FDR <0.05 in at least 1 of the comparisons are shown. (B) Violin plot of TNF-α signaling via NF-κB pathway signature in CD8⁺ memory T cells from patients with SCROT and NSR at baseline (left). Enrichment plots for TNF-α signaling via NF-κB gene set in the comparison of patients with SCROT vs those with NSR (right). (C) Dot plots showing expression of expressed genes from TNF-α signaling via NF-κB gene set in CD8⁺ memory T cells from patients with SCROT and NSR at baseline. Dot sizes represent the percentage of cluster cells in which transcripts for that gene are detected. Dot color represents the average expression level (scaled normalized counts) of that gene in the population. Percentages of CD3⁺CD8⁺CD69⁺ (D) or CD3⁺CD4⁺CD69⁺ (E) T cells assessed via flow cytometry after overnight resting at baseline for patients with SCROT, SROT, and NSR. Bars indicate median. The Kruskal-Wallis and Wilcoxon-Mann-Whitney tests were used as appropriate. Only significant P values are reported; ∗∗P < .01.