Figure 3.

Longitudinal CyTOF profiling of patient PBMCs reveals NAC-induced enrichment of NK cell populations associated with clinical response. A, Schematic of CyTOF study. B (i), t-SNE analysis of matched PBMC samples from patients with RD (n = 4) and pCR (n = 4) at baseline, on-treatment, and post-surgery showing the identification of major immune cell families. B (ii and iii), Log₂ FC in the abundance of each cell population on treatment (n = 8) and post-surgery (n = 14), compared with baseline, among patients with B (ii) pCR and B (iii) RCB II/III disease; LIMMA test. P values represent those which showed statistical significance in at least 3 of the 4 seeds tested, with a |log₂ fold change (FC)| > 1.5. B (iv) and B (v), Log₂FC in proportions of major immune cell families on-treatment [B (iv); n = 8] and post-surgery [(B (v); n = 14], normalized to baseline proportions (LIMMA). C, Proportion of CD16⁺ and CD16- NK cell clusters at baseline among patients with RD and pCR (n = 14). LIMMA test. D, Proportion of CD16⁺ and CD16^– NK cell clusters on-treatment among patients with RD and pCR (n = 14). LIMMA test. E, FACS gating strategy of manually gated CD3^– CD19^–CD123^–CD56⁺ NK cells showing identification of 4 NK cell subsets based on CD56 and CD16 expression. F, Baseline peripheral NK cell subsets among patients who went on to achieve pCR or RD after NAC and healthy donors (Mann–Whitney U test; ***, P ≤ 0.0001). G, Peripheral NK cell subsets at “on-treatment” time point from patients who went on to achieve pCR or RD after NAC (Mann–Whitney U test; *, P ≤ 0.05). H, Peripheral NK cell subsets at the “post-surgical” timepoint among patients who achieved pCR or RD after NAC (Mann–Whitney U test; ns P > 0.05).