Supplementary Figure 2 Supplementary Figure 2. White blood cell differential count White blood cell (WBC) differential counts were analyzed from patients at the time of discontinuation (baseline) and at 1 month (1mo) after stopping imatinib therapy. Results are reported as absolute (upper row) and relative values (lower row). Paired non-parametrical t-test was performed to compare the baseline and 1 month groups statistically.

Supplementary Figure 3 Supplementary Figure 3. Lymphocyte subclass analysis in patients and healthy controls Lymphocyte subclasses (CD3+ T cells, CD4+ and CD8+ T cells, CD19+ B cells and CD16/56+CD3- NK cells) were measured with flow cytometry from CML patients at the time of imatinib discontinuation (baseline) and 1 month after stopping (1mo) as well as from healthy controls. Results are reported as absolute (A-E) and relative values (F-J). Paired non-parametrical t-test was performed to compare the baseline and 1 month groups and Mann-Whitney test when compared baseline to healthy.

Supplementary Figure 4 Supplementary Figure 4. The relative and absolute number of NK cells at 1 month time point after imatinib discontinuation. A) The relative number of NK cells at 1 month in patient groups D) Absolute NK cell count at 1 month in patient groups. Box-and-whisker plots present 5-95 percentiles. One-way Anova was used for comparison between multiple groups (exact p-value reported in the figure), and Bonferroni’s post test was used to compare selected pairs (only early relapse group was compared to late and non-relapse groups). *p<0.05, **p<0.01.

Supplementary Figure 5 Supplementary Figure 5. NK cell phenotype at 1month after imatinib discontinuation Ficoll isolated fresh PB MNCs were analyzed with multicolor flow cytometry. NK cells were defined as CD3-CD56+ lymphocytes. A) The proportion of CD56DIM cells of NK cells in early, late and non-relapsing) patients. B) The proportion of CD57+ NK cells. C) The proportion of CD16+ of NK cells. One-way Anova was used for comparison between multiple groups (exact p-value reported in the figure), and Bonferroni’s post test was used to compare selected pairs (only early relapse group was compared to late and non-relapse groups). *p<0.05

Supplementary Figure 6 Supplementary Figure 6. NK cell receptor expression at baseline and 1 month after imatinib discontinuation. Median fluorescent intensities from CD3-CD56dim population were measured with flow cytometry from CML patients at the time of imatinib discontinuation (baseline) and 1 month after stopping (1mo).

Supplementary Figure 7 Supplementary Figure 7. Schematic figure presenting the hypothesis of the role of NK and T cells in TKI discontinuation Direct contact of NK cells with leukemia cells or cytokines derived from activated antigen presenting cells (APCs) can result in NK cell proliferation and maturation. After repeated stimulus, a fraction of NK cells may differentiate into the adaptive-like NK cells. NK cells are able to both directly kill the leukemia cells by recognizing them with their activating receptors (NKG2D, NKp30 and NKp46) and to promote the Th1 type of T cell responses. In the late relapsing group adaptive T cell responses maybe impaired. In the early relapsing group no specific immune response against leukemia exists at all or cells are dysfunctional and leukemia cells have escaped underneath the control of the immune system.