Fig 2: Phenotypic maturation reflects repertoire focusing which is independent of the CDR3δ traits. (A) Proportion of Vδ2TCR+ T cells among CD3+ cells in the donors of different phenotypic profiles. (B) Correlation matrix showing Spearman’s correlation coefficients for the proportion of Vδ2+ T cells among CD3+ T cells, and the proportion of CD27+, CD28+, or CD16+ T cells among Vδ2+ T cells, measured in an independent set of 10 healthy donors. (C–E) Measures of diversity: Shannon entropy (C), repertoire richness (number of individual clonotypes, (D), and repertoire evenness, defined as D75 (E) in the late-stage profile donors (n = 4). (F–H) Proportion of sequences featuring the determinants of pAg reactivity: rearrangement to J1 region (F), the invT (G), and a hydrophobic AA5 (H) among the clonotypes with increasing frequency f in the CD27neg cell population of the late-stage donors. Bars represent median values and IQRs. The median difference and the p-values were determined using Wilcoxon rank-sum test. *p < 0.05; **p ≤ 0.01; ***p ≤ 0.001. (I) CDR3δ length distribution among J1-rearranged clonotypes in the CD27neg cells. Sequences were classified by f. Lines connect the mean abundances of clonotypes of each respective length within the frequency category.

Fig 3: Human CD69+CD16− lung NK cell subsets have unique characteristics. a Representative overlays and b summary of data of expression of NKG2A and CD57 on CD16− human lung CD69−CD49a−CD103− (n = 20 for both), CD69sp (n = 20 for both), CD69+CD49a+CD103− (n = 14 and n = 13, respectively), and CD69+CD49a+CD103+ (n = 17 and n = 15, respectively) NK cells. CD56dimCD16+ NK cells are shown for comparison (n = 20 and n = 19, respectively). Numbers in a indicate %NKG2A+ and %CD57+ NK cells, respectively. c Representative overlays and d summary of mean fluorescence intensity (MFI) of CD56 (n = 18 for CD16−CD69−CD49a−CD103−NKG2A+CD57−, n = 21 for CD69+CD49a−CD103−CD16−, n = 16 for CD69+CD49a+CD103−CD16−, n = 19 for CD69+CD49a+CD103+CD16−, and n = 20 for CD56dimCD16+), CXCR3 (n = 3) and CXCR6 (n = 7) on human lung CD69−CD49a−CD103−NKG2A+CD57−, CD69sp, CD69+CD49a+CD103−, and CD69+CD49a+CD103+ NK cells within the CD16− subset. e Representative overlay and f summary of MFI of perforin expression in CD16−CD69−CD49a−CD103−NKG2A+CD57−, CD69spCD16−, CD69+CD49a+CD103−CD16−, CD69+CD49a+CD103+ CD16−, and CD69−CD49a−CD103−CD16+ NK cells in human lung (n = 5). CD127+CD161+ cells from lung tissue are shown as a comparison (n = 5). g Representative overlays and h summary of MFI of Eomes (left panel) (CD16−CD69−CD49a−CD103−NKG2A+CD57− (n = 5, other subsets n = 7) and T-bet (right panel) (CD16−CD69−CD49a−CD103−NKG2A+CD57− (n = 4, other subsets n = 6) expression in CD16− human lung CD69−CD49a−CD103−NKG2A+CD57−, CD69sp, CD69+CD49a+CD103−, and CD69+CD49a+CD103+ NK cells. Expression in CD16+CD69−CD49a−CD103− NK cells and non-NK cell ILCs (CD56−CD16−NKG2A−KIR−CD161+) are shown as a reference for Eomes (n = 4), and T-bet (n = 6), respectively. i Principal component analysis based on 1,000 most variable genes across subsets. j Euler diagram based on the 230 differentially expressed genes (DEGs, p < 0.05, log2 fold change > 1) between CD69+CD49a+CD103+NKG2A+CD16−, CD69+CD49a+CD103−NKG2A+CD16−, CD69spNKG2A+CD16− and CD69−NKG2A+CD16− NK cells. DEGs among CD69+CD49a+CD103+NKG2A+CD16− and CD69+CD49a+CD103−NKG2A+CD16− were pooled in the analysis. k Heatmap of 142 DEGs (padj < 0.01, log2 fold change > 1) with genes ordered by hierarchical clustering. Genes involved in regulation of tissue-residency, homing, and/or NK cell function are highlighted. Two replicates per donor and subsets are shown. Significant DEGs identified using deSeq2. Colour scale depicts z-score. b, d, f, h Kruskal-Wallis test, Dunn’s multiple comparisons test, *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001. Means ± SD are shown. Source data are provided as a Source Data file

Fig 4: Monocyte population displays epichaperome abundance and immunophenotyped changes during the course of treatment with PU-H71 while T lymphocytes are not affected.a Epichaperome abundance in monocytes and CD3 + T-cell lymphocytes in WCM254 compared with normal PB lymphocytes (NPB). Graph, mean ± SD of MFI of monocytes/MFI of CD3 + lymphocytes. b Representative monocyte subsets (classical, intermediate, and non-classical) based on CD14 and CD16 expression in normal healthy donor (left). Chronological changes in monocyte subsets in patient WCM254 during PU-H71 therapy (right). Pro-inflammatory subsets CD14highCD16 + (intermediate) and CD14lowCD16 + (non-classical) decreased after PU-H71 treatment reflecting proportions similar to normal monocyte subsets. c Phenotyping of T-lymphocytes in WCM254 at baseline, day 25 and day 32, with representative T cells from a healthy donor shown on the left. Proportion of CD4 + and CD8 + T lymphocytes and naive/central memory/effector/terminally differentiated effector T cells of each CD4 + and CD8 + T cells did not show changes in WCM254 under PU-H71 treatment (right three columns).

Fig 5: CD69+CD16− NK cells in the human lung co-express CD49a and CD103. a Representative dot plots and b summary of data of CD49a and CD103 expression on CD69+CD16− and CD69+CD16+ NK cells (n = 64). Mean ± SD is shown. c Linear regression analysis of CD49a and CD103 co-expression on NK cells in human lung (n = 98). d Representative histogram and e summary of data of CD16 expression on CD69− (n = 20), CD69sp (n = 20), and CD69+CD49a+CD103− (n = 17), CD69+CD49a−CD103+ (n = 15) and CD69+CD49a+CD103+ (n = 19) NK cells in human lung. Mean ± SD is shown. f Summary of data for CD69 expression on human lung CD49a−CD103−CD16− (orange), CD49a+CD103−CD16−, CD49a−CD103+CD16−, and CD49a+CD103+CD16− (all blue) NK cells (n = 37). Mean ± SD is shown. g Frequency of NK cell subsets defined by the expression of CD16, CD69, CD49a, and CD103 out of total NK cells (n = 37). Mean ± SD is shown h Percentages of CD49a+ and i CD103+ cells among CD127+ ILCs (defined as live CD45+CD14−CD19−CD3−CD16−NKG2A−KIR−CD69+CD127+) (n = 19) and CD69+CD8+ T cells in the human lung (n = 23). Mean ± SD is shown. Statistical analysis in b, f RM one-way ANOVA, Tukey’s multiple comparison test, Geisser-Greenhouse’s correction. *p < 0.05, **p < 0.005, ***p < 0.001, ****p < 0.0001; ns, non-significant; e Kruskall-Wallis test, Dunn’s multiple comparisons test. **p < 0.005, ****p < 0.0001; h, i Two-tailed Wilcoxon matched-pairs signed rank test, ****p < 0.0001. Source data are provided as a Source Data file